Discussion:
[gmx-users] Ion concentration of genion vs charmm-gui
Ali Khan
2014-05-13 18:52:45 UTC
Permalink
Hey,

I generated a membrane in charmm-gui that I will be simulating in gromacs.
I am using genion to add 0.14 M potassium by using the -conc flag. In a box
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion number
I should go with?

Best Wishes,
Ali Khan
Mark Abraham
2014-05-13 19:38:37 UTC
Permalink
Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.

Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in gromacs.
I am using genion to add 0.14 M potassium by using the -conc flag. In a box
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion number
I should go with?
Best Wishes,
Ali Khan
--
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Antonio Baptista
2014-05-13 20:20:09 UTC
Permalink
Actually, your target concentration usually refers to the macroscopic
solution bulk, not to the simulation box. Therefore, it is generally more
correct to think in terms of the ion:solvent molar ratios -- that is, turn
your molar concentration into the corresponding macroscopic ion:solvent
molar ratios, and then use those ratios in your box.

In many cases it doesn't make much difference which approach you use,
because the fraction of box volume occupied by the non-solvent part of the
simulated system is often very small. However, a membrane typically
occupies a substantial volume of your box, so I would advise the molar
fraction approach in your case.

(Strictly speaking, not even that is necessarily correct, because your
system of interest may induce a local ion concentration different from the
bulk one. But that is an entirely different issue.)

Best,
Antonio
Post by Mark Abraham
Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.
Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in gromacs.
I am using genion to add 0.14 M potassium by using the -conc flag. In a box
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion number
I should go with?
Best Wishes,
Ali Khan
--
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--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619 email: baptista at itqb.unl.pt
fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista
--------------------------------------------------------------------------
Ali Khan
2014-05-14 03:11:33 UTC
Permalink
Sorry Mark,

I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232 potassium
atoms. Its a small difference, and both methods have the same box size.
Post by Mark Abraham
Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.
Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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Erik Marklund
2014-05-14 15:14:55 UTC
Permalink
Hi Ali,

And what would you expect in this case, based on the definition of concentration?

Erik
Post by Ali Khan
Sorry Mark,
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232 potassium
atoms. Its a small difference, and both methods have the same box size.
Post by Mark Abraham
Sounds like a problem for a high-school chemistry test ;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.
Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui, the
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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Ali Khan
2014-05-14 16:06:16 UTC
Permalink
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.


On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
Post by Erik Marklund
Hi Ali,
And what would you expect in this case, based on the definition of concentration?
Erik
Post by Ali Khan
Sorry Mark,
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
potassium
Post by Ali Khan
atoms. Its a small difference, and both methods have the same box size.
On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com
Post by Mark Abraham
Sounds like a problem for a high-school chemistry test ;-)
concentration =
Post by Ali Khan
Post by Mark Abraham
quantity / volume. From the factor of ~1000, probably you're inputting
box
Post by Ali Khan
Post by Mark Abraham
sizes in A instead of nm, or vice-versa, somewhere.
Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui,
the
Post by Ali Khan
Post by Mark Abraham
Post by Ali Khan
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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Justin Lemkul
2014-05-14 17:06:41 UTC
Permalink
Post by Ali Khan
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.
Better yet, please report it to the CHARMM-GUI people. If there's something
wrong, it needs to be fixed. There is a very easy email form to fill out to
report issues.

-Justin
Post by Ali Khan
On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
Post by Erik Marklund
Hi Ali,
And what would you expect in this case, based on the definition of concentration?
Erik
Post by Ali Khan
Sorry Mark,
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
potassium
Post by Ali Khan
atoms. Its a small difference, and both methods have the same box size.
On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com
Post by Mark Abraham
Sounds like a problem for a high-school chemistry test ;-)
concentration =
Post by Ali Khan
Post by Mark Abraham
quantity / volume. From the factor of ~1000, probably you're inputting
box
Post by Ali Khan
Post by Mark Abraham
sizes in A instead of nm, or vice-versa, somewhere.
Mark
Post by Ali Khan
Hey,
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui,
the
Post by Ali Khan
Post by Mark Abraham
Post by Ali Khan
server stated that I should add 232 potassium ions to reach a 0.14 M
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================
Ali Khan
2014-05-14 17:15:35 UTC
Permalink
I just did. It turns out that when there is a charged lipid in the system
(as in my case), charmm-gui increases the effective concentration to
compensate for the system's net charge. I have pasted my discourse with
them below.

My email:
I have a question. I generated a membrane using the charmm-gui membrane
builder. The server generated a 2POPC:1POPS bilayer in a box with water.
The box dimensions were 135.355 A x 135.355 A x 130 A. I asked membrane
builder to added 140 mM KCl, and it recommended 232 positive ions and 46
negative ions. I also made this ion calculation by hand using the volume of
the box, and my calculation gave me 201 positive ions for 0.14 M. If I
calculated the concentration of ions based solely on the amount of water
molecules in the box (54682 water molecules), I obtain 139 positive ions to
make 0.14 M. I am trying to figure out where is the discrepancy is.

Reply:
The discrepancy arises from the net charge of the system since you have PS
lipid types. So, your effective concentration should be higher to
compensate such system net charge.
Post by Justin Lemkul
Post by Ali Khan
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.
Better yet, please report it to the CHARMM-GUI people. If there's
something wrong, it needs to be fixed. There is a very easy email form to
fill out to report issues.
-Justin
Post by Ali Khan
On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <
erik.marklund at chem.ox.ac.uk
Hi Ali,
Post by Erik Marklund
And what would you expect in this case, based on the definition of concentration?
Erik
Sorry Mark,
Post by Ali Khan
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
potassium
Post by Ali Khan
atoms. Its a small difference, and both methods have the same box size.
On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com
Sounds like a problem for a high-school chemistry test ;-)
concentration =
quantity / volume. From the factor of ~1000, probably you're inputting
box
sizes in A instead of nm, or vice-versa, somewhere.
Post by Ali Khan
Mark
Hey,
Post by Ali Khan
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui,
the
server stated that I should add 232 potassium ions to reach a 0.14 M
Post by Ali Khan
Post by Ali Khan
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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Justin Lemkul
2014-05-15 16:02:01 UTC
Permalink
Post by Ali Khan
I just did. It turns out that when there is a charged lipid in the system
(as in my case), charmm-gui increases the effective concentration to
compensate for the system's net charge. I have pasted my discourse with
them below.
If this is the case, I would expect genion to do the same thing, but you need to
specify the behavior manually. Did you use the -neutral flag when running
genion, or did you just specify -conc? The combination of -neutral and -conc
0.14 should have given the same number of excess ions. 201 is the number of
ions expected for a box of that size that is already neutral.

-Justin
Post by Ali Khan
I have a question. I generated a membrane using the charmm-gui membrane
builder. The server generated a 2POPC:1POPS bilayer in a box with water.
The box dimensions were 135.355 A x 135.355 A x 130 A. I asked membrane
builder to added 140 mM KCl, and it recommended 232 positive ions and 46
negative ions. I also made this ion calculation by hand using the volume of
the box, and my calculation gave me 201 positive ions for 0.14 M. If I
calculated the concentration of ions based solely on the amount of water
molecules in the box (54682 water molecules), I obtain 139 positive ions to
make 0.14 M. I am trying to figure out where is the discrepancy is.
The discrepancy arises from the net charge of the system since you have PS
lipid types. So, your effective concentration should be higher to
compensate such system net charge.
Post by Justin Lemkul
Post by Ali Khan
By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.
Better yet, please report it to the CHARMM-GUI people. If there's
something wrong, it needs to be fixed. There is a very easy email form to
fill out to report issues.
-Justin
Post by Ali Khan
On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <
erik.marklund at chem.ox.ac.uk
Hi Ali,
Post by Erik Marklund
And what would you expect in this case, based on the definition of concentration?
Erik
Sorry Mark,
Post by Ali Khan
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
potassium
Post by Ali Khan
atoms. Its a small difference, and both methods have the same box size.
On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com
Sounds like a problem for a high-school chemistry test ;-)
concentration =
quantity / volume. From the factor of ~1000, probably you're inputting
box
sizes in A instead of nm, or vice-versa, somewhere.
Post by Ali Khan
Mark
Hey,
Post by Ali Khan
I generated a membrane in charmm-gui that I will be simulating in
gromacs.
Post by Ali Khan
I am using genion to add 0.14 M potassium by using the -conc flag. In a
box
Post by Ali Khan
with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
should add 201 K atoms. When I constructed the system in charmm-gui,
the
server stated that I should add 232 potassium ions to reach a 0.14 M
Post by Ali Khan
Post by Ali Khan
concentration. Does anyone have a suggestion of which potassium ion
number
Post by Ali Khan
I should go with?
Best Wishes,
Ali Khan
--
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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