Discussion:
[gmx-users] mdrun-adjusted cutoffs?!
Alex
2018-12-04 22:35:17 UTC
Permalink
Hi all,

We've long noticed that at the beginning of simulations mdrun goes through
what seems like trying to adjust the short-range NB radii to its liking.
What is up with that and does this mean that every simulation proceeds with
a new cutoff? If so, is there a way to disable this?

Thank you,

Alex
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Mark Abraham
2018-12-05 22:36:36 UTC
Permalink
Hi,

There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things? We're
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!

Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes through
what seems like trying to adjust the short-range NB radii to its liking.
What is up with that and does this mean that every simulation proceeds with
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
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Alex
2018-12-05 22:56:19 UTC
Permalink
Hi Mark,

I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.

I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.

Thank you,

Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things? We're
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes through
what seems like trying to adjust the short-range NB radii to its liking.
What is up with that and does this mean that every simulation proceeds with
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
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posting!
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Mark Abraham
2018-12-06 05:34:51 UTC
Permalink
Hi,

One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system is
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. Electrostatic
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.

Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its liking.
What is up with that and does this mean that every simulation proceeds
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
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Alex
2018-12-06 10:08:58 UTC
Permalink
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.

I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.

Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system is
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. Electrostatic
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its liking.
What is up with that and does this mean that every simulation proceeds
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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Mark Abraham
2018-12-06 12:42:28 UTC
Permalink
Hi,

It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the question
at hand?

Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation proceeds
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Alex
2018-12-06 19:39:03 UTC
Permalink
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.

Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the question
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation proceeds
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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Mark Abraham
2018-12-07 04:38:55 UTC
Permalink
Hi,

Zero, because we are shifting between equivalent ways to compute the total
electrostatic interaction.

You can turn off the PME tuning with mdrun -notunepme, but unless there's a
bug, all that will do is force it to run slower than optimal. Obviously you
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.

Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors,
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
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Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Alex
2018-12-07 06:09:45 UTC
Permalink
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the total
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless there's a
bug, all that will do is force it to run slower than optimal. Obviously you
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors,
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
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Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Szilárd Páll
2018-12-07 14:58:42 UTC
Permalink
BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.

--
Szilárd
Post by Alex
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the total
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless there's a
bug, all that will do is force it to run slower than optimal. Obviously you
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors,
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair searching
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies things?
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if you
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
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Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Mark Abraham
2018-12-08 20:34:42 UTC
Permalink
Hi,

Note that that will compare runs of differently accurate electrostatic
approximation. For iso-accurate comparisons, one must also scale the
Fourier grid by the same factor (per the manual section on PME autotuning).
Of course, if you start from the smallest rcoulomb and use a fixed grid,
then the comparisons will be of increasing accuracy, which might be enough
for the desired conclusion.

Mark
Post by Szilárd Páll
BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.
--
Szilárd
Post by Alex
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the
total
Post by Alex
Post by Mark Abraham
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless
there's a
Post by Alex
Post by Mark Abraham
bug, all that will do is force it to run slower than optimal.
Obviously you
Post by Alex
Post by Mark Abraham
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how
much
Post by Alex
Post by Mark Abraham
Post by Alex
the free energy of ionic hydration for K+ changes in, say, a system
that
Post by Alex
Post by Mark Abraham
Post by Alex
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least
temporarily.
Post by Alex
Post by Mark Abraham
Post by Alex
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about,
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
LJ portion contributes ~20% at the most. When the change in
energetics
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can
easily
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
envision someone doing ion permeation across KcsA and the currents
would
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
be similarly affected. For instance, when I set all cutoffs at 1.0
nm,
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
mdrun ends up using something like 1.1 nm for electrostatics, at
least
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally
arbitraty and
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
then often requires crutches elsewhere, but my question was whether
for
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
very sensitive quantities mdrun ends up utilizing the forcefield as
it
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
was designed and not in a "slightly off" regime. Basically, you
asked me
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient
overall
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay
out my
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what
we
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
normally mean by diffusive permeation. Instead, there are
considerable
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent.
It is
Post by Alex
Post by Mark Abraham
Post by Alex
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular
cutoff
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
value and our results are rather sensitive to that. I can't say
we're
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative
behaviors,
Post by Alex
Post by Mark Abraham
Post by Alex
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in
cutoffs.
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair
searching
Post by Alex
Post by Mark Abraham
Post by Alex
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies
things?
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if
you
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun
goes
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
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Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Post by Alex
Post by Mark Abraham
Post by Alex
or
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Post by Alex
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Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Post by Alex
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Alex
2018-12-08 20:45:35 UTC
Permalink
That's very valuable info, thank you.

By the way, all of our production mdp files have something like
fourierspacing = 0.135, the origin of which is long gone from my memory.
Does this imply that despite PME tuning our simulations use a fixed
Fourier grid that ends up in suboptimal performance, or does the tuning
override it?

Alex
Post by Mark Abraham
Hi,
Note that that will compare runs of differently accurate electrostatic
approximation. For iso-accurate comparisons, one must also scale the
Fourier grid by the same factor (per the manual section on PME autotuning).
Of course, if you start from the smallest rcoulomb and use a fixed grid,
then the comparisons will be of increasing accuracy, which might be enough
for the desired conclusion.
Mark
Post by Szilárd Páll
BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.
--
Szilárd
Post by Alex
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the
total
Post by Alex
Post by Mark Abraham
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless
there's a
Post by Alex
Post by Mark Abraham
bug, all that will do is force it to run slower than optimal.
Obviously you
Post by Alex
Post by Mark Abraham
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how
much
Post by Alex
Post by Mark Abraham
Post by Alex
the free energy of ionic hydration for K+ changes in, say, a system
that
Post by Alex
Post by Mark Abraham
Post by Alex
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least
temporarily.
Post by Alex
Post by Mark Abraham
Post by Alex
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about,
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
LJ portion contributes ~20% at the most. When the change in
energetics
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can
easily
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
envision someone doing ion permeation across KcsA and the currents
would
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
be similarly affected. For instance, when I set all cutoffs at 1.0
nm,
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
mdrun ends up using something like 1.1 nm for electrostatics, at
least
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally
arbitraty and
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
then often requires crutches elsewhere, but my question was whether
for
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
very sensitive quantities mdrun ends up utilizing the forcefield as
it
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
was designed and not in a "slightly off" regime. Basically, you
asked me
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
to describe our case and why I think there may be a slight issue, so
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient
overall
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay
out my
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what
we
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
normally mean by diffusive permeation. Instead, there are
considerable
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent.
It is
Post by Alex
Post by Mark Abraham
Post by Alex
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular
cutoff
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
value and our results are rather sensitive to that. I can't say
we're
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative
behaviors,
Post by Alex
Post by Mark Abraham
Post by Alex
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in
cutoffs.
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair
searching
Post by Alex
Post by Mark Abraham
Post by Alex
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies
things?
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if
you
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun
goes
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to its
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
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Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
posting!
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Post by Alex
Post by Mark Abraham
Post by Alex
or
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Post by Alex
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Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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Post by Alex
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Mark Abraham
2018-12-10 05:56:44 UTC
Permalink
Hi,

There's two ways to specify the long-range grid requirements (either
fourierspacing, or fourier-nx and friends,, see
http://manual.gromacs.org/documentation//current/user-guide/mdp-options.html#ewald).
The tuning will override fourierspacing in the same way that it does
rcoulomb. I assume it does not override a manual specification of the grid
dimensions, but I haven't tried it. Have noted to the dev team that we
should check and document that.

Mark
Post by Alex
That's very valuable info, thank you.
By the way, all of our production mdp files have something like
fourierspacing = 0.135, the origin of which is long gone from my memory.
Does this imply that despite PME tuning our simulations use a fixed
Fourier grid that ends up in suboptimal performance, or does the tuning
override it?
Alex
Post by Mark Abraham
Hi,
Note that that will compare runs of differently accurate electrostatic
approximation. For iso-accurate comparisons, one must also scale the
Fourier grid by the same factor (per the manual section on PME
autotuning).
Post by Mark Abraham
Of course, if you start from the smallest rcoulomb and use a fixed grid,
then the comparisons will be of increasing accuracy, which might be
enough
Post by Mark Abraham
for the desired conclusion.
Mark
Post by Szilárd Páll
BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.
--
Szilárd
Post by Alex
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the
total
Post by Alex
Post by Mark Abraham
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless
there's a
Post by Alex
Post by Mark Abraham
bug, all that will do is force it to run slower than optimal.
Obviously you
Post by Alex
Post by Mark Abraham
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how
much
Post by Alex
Post by Mark Abraham
Post by Alex
the free energy of ionic hydration for K+ changes in, say, a system
that
Post by Alex
Post by Mark Abraham
Post by Alex
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least
temporarily.
Post by Alex
Post by Mark Abraham
Post by Alex
Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
Post by Mark Abraham
at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about,
the
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
LJ portion contributes ~20% at the most. When the change in
energetics
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can
easily
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
envision someone doing ion permeation across KcsA and the currents
would
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
be similarly affected. For instance, when I set all cutoffs at 1.0
nm,
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
mdrun ends up using something like 1.1 nm for electrostatics, at
least
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally
arbitraty and
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
then often requires crutches elsewhere, but my question was whether
for
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
very sensitive quantities mdrun ends up utilizing the forcefield as
it
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
was designed and not in a "slightly off" regime. Basically, you
asked me
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
to describe our case and why I think there may be a slight issue,
so
Post by Mark Abraham
Post by Szilárd Páll
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
of traditional lengths cause approximation errors that cause
compensating
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
parameterization errors elsewhere; those effects get worse if the
system
Post by Mark Abraham
Post by Alex
is
Post by Mark Abraham
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
Post by Mark Abraham
with PME is quite another matter - there you need sufficient
overall
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay
out my
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which
the
Post by Mark Abraham
Post by Szilárd Páll
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
quantity of interest is ion current via pores that disallow what
we
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
normally mean by diffusive permeation. Instead, there are
considerable
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent.
It is
Post by Alex
Post by Mark Abraham
Post by Alex
my
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
understanding that NB stuff gets parameterized at a particular
cutoff
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
value and our results are rather sensitive to that. I can't say
we're
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative
behaviors,
Post by Alex
Post by Mark Abraham
Post by Alex
but
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
of NB energy variation as a function of small differences in
cutoffs.
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair
searching
Post by Alex
Post by Mark Abraham
Post by Alex
in
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
section 3.4.2 of the reference manual. Perhaps that clarifies
things?
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
We're
Post by Mark Abraham
not aware of a reason to want to control things manually, but if
you
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
have
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun
goes
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
through
Post by Mark Abraham
Post by Alex
what seems like trying to adjust the short-range NB radii to
its
Post by Mark Abraham
Post by Szilárd Páll
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
liking.
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
What is up with that and does this mean that every simulation
proceeds
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
with
Post by Mark Abraham
Post by Alex
a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
posting!
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Post by Mark Abraham
Post by Szilárd Páll
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
Post by Mark Abraham
Post by Alex
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or
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Post by Alex
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Post by Alex
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Szilárd Páll
2018-12-10 14:07:10 UTC
Permalink
Post by Mark Abraham
Hi,
There's two ways to specify the long-range grid requirements (either
fourierspacing, or fourier-nx and friends,, see
http://manual.gromacs.org/documentation//current/user-guide/mdp-options.html#ewald).
The tuning will override fourierspacing in the same way that it does
rcoulomb. I assume it does not override a manual specification of the grid
dimensions, but I haven't tried it. Have noted to the dev team that we
should check and document that.
If PME tuning as active, it will try to shift work from PME to PP
regardless of the means used to specify the PME settings (spacing or
explicit grid). I think that's consistent with the docs, isn't it?
Post by Mark Abraham
Mark
Post by Alex
That's very valuable info, thank you.
By the way, all of our production mdp files have something like
fourierspacing = 0.135, the origin of which is long gone from my memory.
Does this imply that despite PME tuning our simulations use a fixed
Fourier grid that ends up in suboptimal performance, or does the tuning
override it?
Alex
Post by Mark Abraham
Hi,
Note that that will compare runs of differently accurate electrostatic
approximation. For iso-accurate comparisons, one must also scale the
Fourier grid by the same factor (per the manual section on PME
autotuning).
Post by Mark Abraham
Of course, if you start from the smallest rcoulomb and use a fixed grid,
then the comparisons will be of increasing accuracy, which might be
enough
Post by Mark Abraham
for the desired conclusion.
Mark
Post by Szilárd Páll
BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.
--
Szilárd
Post by Alex
I think that answers my question, thanks. :)
Post by Mark Abraham
Hi,
Zero, because we are shifting between equivalent ways to compute the
total
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electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless
there's a
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bug, all that will do is force it to run slower than optimal.
Obviously you
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could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark
Post by Alex
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how
much
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the free energy of ionic hydration for K+ changes in, say, a system
that
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contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least
temporarily.
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Alex
Post by Mark Abraham
Hi,
It sounds like you are only looking at the short-ranged component of
the
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electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the
question
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at hand?
Mark
Post by Alex
More specifically, electrostatics. For the stuff I'm talking about,
the
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LJ portion contributes ~20% at the most. When the change in
energetics
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is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can
easily
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envision someone doing ion permeation across KcsA and the currents
would
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be similarly affected. For instance, when I set all cutoffs at 1.0
nm,
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mdrun ends up using something like 1.1 nm for electrostatics, at
least
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that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally
arbitraty and
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then often requires crutches elsewhere, but my question was whether
for
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very sensitive quantities mdrun ends up utilizing the forcefield as
it
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was designed and not in a "slightly off" regime. Basically, you
asked me
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to describe our case and why I think there may be a slight issue,
so
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Post by Szilárd Páll
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there it is.
Alex
Post by Mark Abraham
Hi,
One needs to be more specific than NB. There is evidence that VDW
cutoffs
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of traditional lengths cause approximation errors that cause
compensating
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parameterization errors elsewhere; those effects get worse if the
system
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is
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inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Electrostatic
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with PME is quite another matter - there you need sufficient
overall
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accuracy, and there are multiple equivalent ways to do that.
Mark
Post by Alex
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay
out my
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thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which
the
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quantity of interest is ion current via pores that disallow what
we
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normally mean by diffusive permeation. Instead, there are
considerable
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barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent.
It is
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my
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understanding that NB stuff gets parameterized at a particular
cutoff
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value and our results are rather sensitive to that. I can't say
we're
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dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist
between
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something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative
behaviors,
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but
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I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing
estimates
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of NB energy variation as a function of small differences in
cutoffs.
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Thank you,
Alex
Post by Mark Abraham
Hi,
There's quite detailed discussion of the treatment of pair
searching
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in
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section 3.4.2 of the reference manual. Perhaps that clarifies
things?
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We're
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not aware of a reason to want to control things manually, but if
you
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have
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one, we're keen to hear of it!
Mark
Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun
goes
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through
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what seems like trying to adjust the short-range NB radii to
its
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Post by Szilárd Páll
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liking.
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What is up with that and does this mean that every simulation
proceeds
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with
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a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
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