Discussion:
[gmx-users] Fatal Equilibration Errors
Nancy
2009-08-08 19:33:17 UTC
Permalink
Hello,

I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation and
equilibration?

I am now trying to run MD on glycerol. I start with a "glycerol.mol2" file
which contains the structure of glycerol. I am using the following commands
to setup and run minimisation and equilibration on glycerol:

$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6

I modified the "defaults" part of the "ffglycerol.itp" (generated by
topolbuild) file to read:

===========================
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
===========================

$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p
glycerol.top -box 2.65 2.65 2.65
$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr

my "em.mdp" file is as follows:

===========================
constraints = none
integrator = steep
nsteps = 10000

emtol = 10.0
emstep = 0.01

nstlist = 2
coulombtype = PME
nstcomm = 2

ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
nstxout = 2

pbc = xyz
pme_order = 4
===========================

$ mdrun -v -deffnm em

the last few lines of output are:

===============================================================
Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5
Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4
Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4
Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4
Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================

As I believe these forces to be acceptable, I proceed to equilibration:

$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr

where my "nvt.mdp" file is:

===========================
title = Glycerol NVT equilibration
define = -DPOSRES

integrator = md
nsteps = 5000
dt = 0.002

nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10

continuation = no
constraint_algorithm = lincs
constraints = all-angles
lincs_iter = 1
lincs_order = 4

ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3

coulombtype = PME
pme_order = 4
fourierspacing = 0.16

tcoupl = V-rescale
tc-grps = GOL SOL
tau_t = 0.1 0.1
ref_t = 300 300

pcoupl = no

pbc = xyz

DispCorr = EnerPres

gen_vel = yes
gen_temp = 300
gen_seed = -1
===========================

where "GOL" refers to GlycerOL.

$ mdrun -v -deffnm nvt

When I execute the above command, I get numerous errors of the following
type:

===============================================================
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.326337, max 0.500490 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'glycerol.pdb in water'
5000 steps, 10.0 ps.

Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.663850, max 1.227203 (between atoms 1 and 7)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 3 172.3 0.2091 0.1644 0.2004
7 9 164.1 0.2082 0.1625 0.2004
2 3 124.5 0.1022 0.0787 0.1000
1 2 148.3 0.1477 0.0882 0.1435
5 6 30.4 0.0992 0.1265 0.1000
8 9 134.1 0.1014 0.0660 0.1000
7 8 138.2 0.1476 0.0991 0.1435

Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger
than the 1-4 table size 2.300 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

There were 12 inconsistent shifts. Check your topology
Segmentation fault
===============================================================

I don't know what is happening wrong. Please advise.

Thank you.

Nancy
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Justin A. Lemkul
2009-08-08 19:49:19 UTC
Permalink
Post by Nancy
Hello,
I have successfully minimised and equilibrated ethylene glycol in a
water box. I have noticed that there seem to be no hydrogen bonds
between the solute and solvent, but there are hydrogen bonds forming and
breaking between solvent molecules. Is this a normal behavior during
minimsation and equilibration?
That will depend on whether or not you are position-restraining your ethylene
glycol, and whether or not your parameters are consistent with the derivation of
the force field.

<snip>
Post by Nancy
Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
These values appear to be reasonable, yes.
Post by Nancy
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
rvdw = 1.3
As I've said before, this value of rvdw is not what is expected when using the
G53a6 parameter set. Unless you've got a good reason for altering the original
force field specifications, generally this is not a good idea.
Post by Nancy
tcoupl = V-rescale
tc-grps = GOL SOL
How many glycerol molecules do you have? If it is only a small fraction of the
system, this treatment of thermostats is likely not appropriate. See here:

http://oldwiki.gromacs.org/index.php/thermostats

<snip>
Post by Nancy
===============================================================
Step 0, time 0 (ps) LINCS WARNING
The procedure for solving a LINCS warning is always the same. Identify where
things start to fall apart, then verify that your topology is correct, and your
.mdp parameters are reasonable. I've made a few comments on .mdp parameters
above. As for the topology, that still remains a mystery. Having never used
topolbuild, I don't know how it assigns parameters, so it may work just fine.
But in general, this is always part of the diagnosis.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Nancy
2009-08-08 20:45:25 UTC
Permalink
While minimising ethylene glycol, I have no defines, and constraints are set
to none. During equilibration, define is set to -DFLEXIBLE, and constraints
are set to all-angles. Which parameters would affect hydrogen bonding?

I have one glycerol molecule in the center of a box of 609 water molecules;
what type of thermostat is reasonable for such a system?


Nancy
Post by Justin A. Lemkul
Post by Nancy
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation and
equilibration?
That will depend on whether or not you are position-restraining your
ethylene glycol, and whether or not your parameters are consistent with the
derivation of the force field.
<snip>
Steepest Descents converged to machine precision in 7007 steps,
Post by Nancy
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
These values appear to be reasonable, yes.
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
rvdw = 1.3
As I've said before, this value of rvdw is not what is expected when using
the G53a6 parameter set. Unless you've got a good reason for altering the
original force field specifications, generally this is not a good idea.
tcoupl = V-rescale
Post by Nancy
tc-grps = GOL SOL
How many glycerol molecules do you have? If it is only a small fraction of
the system, this treatment of thermostats is likely not appropriate. See
http://oldwiki.gromacs.org/index.php/thermostats
<snip>
===============================================================
Post by Nancy
Step 0, time 0 (ps) LINCS WARNING
The procedure for solving a LINCS warning is always the same. Identify
where things start to fall apart, then verify that your topology is correct,
and your .mdp parameters are reasonable. I've made a few comments on .mdp
parameters above. As for the topology, that still remains a mystery.
Having never used topolbuild, I don't know how it assigns parameters, so it
may work just fine. But in general, this is always part of the diagnosis.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
2009-08-08 20:49:26 UTC
Permalink
Post by Nancy
While minimising ethylene glycol, I have no defines, and constraints are
set to none. During equilibration, define is set to -DFLEXIBLE, and
constraints are set to all-angles. Which parameters would affect
hydrogen bonding?
Try "constraints = all-bonds." You should not use -DFLEXIBLE when running dynamics.
Post by Nancy
I have one glycerol molecule in the center of a box of 609 water
molecules; what type of thermostat is reasonable for such a system?
Thermostats require sufficient degrees of freedom to sample a correct
distribution. Coupling one molecule to a thermostat is incorrect. In this
case, "tc-grps = System" is probably reasonable.

-Justin
Post by Nancy
Nancy
On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu
Hello,
I have successfully minimised and equilibrated ethylene glycol
in a water box. I have noticed that there seem to be no
hydrogen bonds between the solute and solvent, but there are
hydrogen bonds forming and breaking between solvent molecules.
Is this a normal behavior during minimsation and equilibration?
That will depend on whether or not you are position-restraining your
ethylene glycol, and whether or not your parameters are consistent
with the derivation of the force field.
<snip>
Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
These values appear to be reasonable, yes.
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
rvdw = 1.3
As I've said before, this value of rvdw is not what is expected when
using the G53a6 parameter set. Unless you've got a good reason for
altering the original force field specifications, generally this is
not a good idea.
tcoupl = V-rescale
tc-grps = GOL SOL
How many glycerol molecules do you have? If it is only a small
fraction of the system, this treatment of thermostats is likely not
http://oldwiki.gromacs.org/index.php/thermostats
<snip>
===============================================================
Step 0, time 0 (ps) LINCS WARNING
The procedure for solving a LINCS warning is always the same.
Identify where things start to fall apart, then verify that your
topology is correct, and your .mdp parameters are reasonable. I've
made a few comments on .mdp parameters above. As for the topology,
that still remains a mystery. Having never used topolbuild, I don't
know how it assigns parameters, so it may work just fine. But in
general, this is always part of the diagnosis.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
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<mailto:gmx-users-request at gromacs.org>.
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Nancy
2009-08-08 21:46:30 UTC
Permalink
Hello,

I have successfully minimised and equilibrated one glycerol molecule in a
box of water (using the ".mdp" files below).

I noticed that during both minimisation and equilibration, solvent molecules
(waters) form many more hydrogen bonds between each other than the solute
(glycerol) forms to the solvent molecules. Is this normal for such a
system?

Thank you.

Nancy


==========em.mdp==========
constraints = none
integrator = steep
nsteps = 10000

emtol = 10.0
emstep = 0.01

nstlist = 2
coulombtype = PME
nstcomm = 2

ns_type = grid
;rlist = 1.0
;rcoulomb = 1.0
;rvdw = 1.0
nstxout = 2

pbc = xyz
pme_order = 4
==========em.mdp==========

==========nvt.mdp==========
title = Glycerol NVT equilibration

integrator = md
nsteps = 5000
dt = 0.002

nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10

continuation = no
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4

ns_type = grid
nstlist = 5

coulombtype = PME
pme_order = 4
fourierspacing = 0.16

tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300

pcoupl = no

pbc = xyz

DispCorr = EnerPres

gen_vel = yes
gen_temp = 300
gen_seed = -1
==========nvt.mdp==========
Post by Justin A. Lemkul
Post by Nancy
While minimising ethylene glycol, I have no defines, and constraints are
set to none. During equilibration, define is set to -DFLEXIBLE, and
constraints are set to all-angles. Which parameters would affect hydrogen
bonding?
Try "constraints = all-bonds." You should not use -DFLEXIBLE when running dynamics.
I have one glycerol molecule in the center of a box of 609 water
Post by Nancy
molecules; what type of thermostat is reasonable for such a system?
Thermostats require sufficient degrees of freedom to sample a correct
distribution. Coupling one molecule to a thermostat is incorrect. In this
case, "tc-grps = System" is probably reasonable.
-Justin
Post by Nancy
Nancy
Hello,
I have successfully minimised and equilibrated ethylene glycol
in a water box. I have noticed that there seem to be no
hydrogen bonds between the solute and solvent, but there are
hydrogen bonds forming and breaking between solvent molecules.
Is this a normal behavior during minimsation and equilibration?
That will depend on whether or not you are position-restraining your
ethylene glycol, and whether or not your parameters are consistent
with the derivation of the force field.
<snip>
Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
These values appear to be reasonable, yes.
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
rvdw = 1.3
As I've said before, this value of rvdw is not what is expected when
using the G53a6 parameter set. Unless you've got a good reason for
altering the original force field specifications, generally this is
not a good idea.
tcoupl = V-rescale
tc-grps = GOL SOL
How many glycerol molecules do you have? If it is only a small
fraction of the system, this treatment of thermostats is likely not
http://oldwiki.gromacs.org/index.php/thermostats
<snip>
===============================================================
Step 0, time 0 (ps) LINCS WARNING
The procedure for solving a LINCS warning is always the same.
Identify where things start to fall apart, then verify that your
topology is correct, and your .mdp parameters are reasonable. I've
made a few comments on .mdp parameters above. As for the topology,
that still remains a mystery. Having never used topolbuild, I don't
know how it assigns parameters, so it may work just fine. But in
general, this is always part of the diagnosis.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org
<mailto:gmx-users-request at gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
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Justin A. Lemkul
2009-08-08 21:52:04 UTC
Permalink
Post by Nancy
Hello,
I have successfully minimised and equilibrated one glycerol molecule in
a box of water (using the ".mdp" files below).
I noticed that during both minimisation and equilibration, solvent
molecules (waters) form many more hydrogen bonds between each other than
the solute (glycerol) forms to the solvent molecules. Is this normal
for such a system?
nsteps = 5000
dt = 0.002
Basing any conclusions on only 10 ps of data collection is likely insufficient.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Nagy, Peter I.
2009-08-08 23:46:59 UTC
Permalink
It is extremely surprising that you have not found solute-solvent hydrogen bonds in aqueous solution. What is the O-C-C-O conformation? If it is trans, then what do the OH hydrogens do?
If O-C-C-O is gauche, then existence of two internal hydrogen bonds is possible, but it is
far from the quantum mechanically most stable form in the gas phase. I think that at least one solute-solvent hydrogen bond should have been seen. There are papers in the literature which do show solute-solvent hydrogen bonds in water. The exciting question is: there is one
H-O-C-C trans moiety in the gas phase, and the other H is H-bonded to this oxygen, when the O-C-C-O skeleton is gauche. Then the question of solvation is, whether this intramolecular hydrogen bond is maintained or disrupts. In aqueous solution it may, whereas in chloroform or CCl4 both OH may be internally H-bonded. Experiments found 12% O-C-C-O trans and 88% O-C-C-O gauche conformers in aqueous solution. Modeling should find what are the positions of the hydroxy hydrogens.
If you really do not find solute-solvent hydrogen bonds, your ethylene-glycol charges may be
questionable. What charge values did you use? A possibility is that the glycol OH charges cannot compete with those of the water model (SPC, TIPxP or what) in forming intermolecular hydrogen bonds.

Peter Nagy
The University of Toledo,
Toledo, OH 43606

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Nancy
Sent: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors

Hello,

I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation and
equilibration?

I am now trying to run MD on glycerol. I start with a "glycerol.mol2" file
which contains the structure of glycerol. I am using the following commands
to setup and run minimisation and equilibration on glycerol:

$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6

I modified the "defaults" part of the "ffglycerol.itp" (generated by
topolbuild) file to read:

===========================
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
===========================

$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p
glycerol.top -box 2.65 2.65 2.65
$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr

my "em.mdp" file is as follows:

===========================
constraints = none
integrator = steep
nsteps = 10000

emtol = 10.0
emstep = 0.01

nstlist = 2
coulombtype = PME
nstcomm = 2

ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
nstxout = 2

pbc = xyz
pme_order = 4
===========================

$ mdrun -v -deffnm em

the last few lines of output are:

===============================================================
Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5
Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4
Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4
Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4
Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================

As I believe these forces to be acceptable, I proceed to equilibration:

$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr

where my "nvt.mdp" file is:

===========================
title = Glycerol NVT equilibration
define = -DPOSRES

integrator = md
nsteps = 5000
dt = 0.002

nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10

continuation = no
constraint_algorithm = lincs
constraints = all-angles
lincs_iter = 1
lincs_order = 4

ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3

coulombtype = PME
pme_order = 4
fourierspacing = 0.16

tcoupl = V-rescale
tc-grps = GOL SOL
tau_t = 0.1 0.1
ref_t = 300 300

pcoupl = no

pbc = xyz

DispCorr = EnerPres

gen_vel = yes
gen_temp = 300
gen_seed = -1
===========================

where "GOL" refers to GlycerOL.

$ mdrun -v -deffnm nvt

When I execute the above command, I get numerous errors of the following
type:

===============================================================
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.326337, max 0.500490 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'glycerol.pdb in water'
5000 steps, 10.0 ps.

Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.663850, max 1.227203 (between atoms 1 and 7)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 3 172.3 0.2091 0.1644 0.2004
7 9 164.1 0.2082 0.1625 0.2004
2 3 124.5 0.1022 0.0787 0.1000
1 2 148.3 0.1477 0.0882 0.1435
5 6 30.4 0.0992 0.1265 0.1000
8 9 134.1 0.1014 0.0660 0.1000
7 8 138.2 0.1476 0.0991 0.1435

Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger
than the 1-4 table size 2.300 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

There were 12 inconsistent shifts. Check your topology
Segmentation fault
===============================================================

I don't know what is happening wrong. Please advise.

Thank you.

Nancy

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Nancy
2009-08-09 20:32:19 UTC
Permalink
Hello,

I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:
http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb

I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF Chimera (
http://www.cgl.ucsf.edu/chimera/).

I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the
topologies:

$ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir
.../topolbuild1_2_2/dat/gromacs -ff gmx53a6

which outputs the files:

ethanediol.gro
ethanediol.log
ethanediolMOL.mol2
ethanediol.top
ffethanediol.itp
posreethanediol.itp

I modified the "ffethanediol.itp" file to read:

=======================================
#define _FF_GROMOS96
#define _FF_GROMOS53A6
#define _FF_USER

[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

#include "ffG53a6nb.itp"
=======================================

The lack of hydrogen bonds between the solute and solvent molecules was due
to the lack of charges in the generated topology file "ethanediol.top". So
I changed the "atoms" section of the topology file (the original topology
file is at the end of this message), and this causes hydrogen bonds between
the solute and solvent in numbers comparable to that between the solvent
molecules.

=======================================
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.17600 14.02700 ;
0.0000000
2 OA 1 EDO O1 1 -0.5740 15.99940 ;
0.0000000
3 H 1 EDO HO1 1 0.39800 1.00800 ;
0.0000000
4 CH2 1 EDO C2 2 0.17600 14.02700 ;
0.0000000
5 OA 1 EDO O2 2 -0.5740 15.99940 ;
0.0000000
6 H 1 EDO HO2 2 0.39800 1.00800 ;
0.0000000
; total molecule charge = 0.0000000
=======================================

I obtained the charge values from the methanol tutoral included with Gromacs
(.../share/gromacs/tutor/methanol/methanol.itp). I then enlarge the box and
solvate the molecule:

$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 2.05 2.05 2.05

$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p
ethanediol.top -box 2.05 2.05 2.05

The solvated system consists of one ethylene glycol and 232 water
molecules. I then configure the minimisation:

$ grompp -f em.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr

with the "em.mdp" file:

=======================================
constraints = none
integrator = steep
nsteps = 10000
;
; Energy minimizing stuff
;

emtol = 2.0
emstep = 0.01

nstlist = 2
coulombtype = PME
nstcomm = 2

ns_type = grid
;rlist = 1.0
;rcoulomb = 1.0
;rvdw = 1.0
nstxout = 2

pbc = xyz
pme_order = 4
=======================================

I then run the minimisation:

$ mdrun -v -deffnm em

The last few lines of output are:

=======================================
Step= 8069, Dmax= 1.5e-04 nm, Epot= -1.22107e+04 Fmax= 8.11110e+01, atom= 5
Step= 8070, Dmax= 1.8e-04 nm, Epot= -1.22107e+04 Fmax= 5.63915e+01, atom= 5
Step= 8071, Dmax= 2.2e-04 nm, Epot= -1.22108e+04 Fmax= 1.20155e+02, atom= 5
Step= 8072, Dmax= 2.6e-04 nm, Epot= -1.22108e+04 Fmax= 7.97799e+01, atom= 5
Step= 8074, Dmax= 1.6e-04 nm, Epot= -1.22108e+04 Fmax= 4.58228e+01, atom= 5
Step= 8078, Dmax= 2.3e-05 nm, Epot= -1.22108e+04 Fmax= 2.84317e+01, atom=
571
Step= 8082, Dmax= 3.5e-06 nm, Epot= -1.22108e+04 Fmax= 2.59027e+01, atom=
571
Step= 8085, Dmax= 1.1e-06 nm, Epot= -1.22108e+04 Fmax= 2.51778e+01, atom= 5
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 2

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 8086 steps,
but did not reach the requested Fmax < 2.
Potential Energy = -1.2210801e+04
Maximum force = 2.5902737e+01 on atom 5
Norm of force = 2.9901226e+00
=======================================

I viewed the minimisation trajectory using VMD, and there are hydrogen bonds
between the solute and solvent.

Then I proceed to equilibration:

$ grompp -f nvt.mdp -c em.gro -p ethanediol.top -o nvt.tpr

where the "nvt.mdp" file is:

=======================================
title = Ethanediol NVT equilibration

integrator = md
nsteps = 50000
dt = 0.002

nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10

continuation = no
constraint_algorithm = lincs
constraints = all-angles
lincs_iter = 1
lincs_order = 4

ns_type = grid
nstlist = 5

coulombtype = PME
pme_order = 4
fourierspacing = 0.16

tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300

pcoupl = no

pbc = xyz

DispCorr = EnerPres

gen_vel = yes
gen_temp = 300
gen_seed = -1
=======================================

I viewed the trajectory of the equilibration, and it looks reasonable. The
O-C-C-O conformation is mostly trans (anti) during the entire NVT
equilibration, and the OH hydrogens form numerous hydrogen bonds with the
solvent (it seems there are no intramolecular hydrogen bonds). Therefore,
the hydrogen bonds do form, given the charges adopted from the methanol
topology (O: -0.574, H: +0.398, CH2: +0.176). Do these charge values seem
reasonable?

The ethylene glycol lacks explicit non-polar hydrogens; is that normal for
this type of system, force field (based on GROMOS96 53a6) and SPC/E water
model?

Thank you.

Nancy




===========ethanediol.top===========
;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "ffethanediol.itp"

[ moleculetype ]
; name nrexcl
EDO_ideal.pdb 3

[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.00000 14.02700 ;
0.0000000
2 OA 1 EDO O1 1 0.00000 15.99940 ;
0.0000000
3 H 1 EDO HO1 1 0.00000 1.00800 ;
0.0000000
4 CH2 1 EDO C2 2 0.00000 14.02700 ;
0.0000000
5 OA 1 EDO O2 2 0.00000 15.99940 ;
0.0000000
6 H 1 EDO HO2 2 0.00000 1.00800 ;
0.0000000
; total molecule charge = 0.0000000

[ bonds ]
; ai aj funct b0 kb
1 4 2 0.15200 5430000. ; C1- C2
4 5 2 0.14350 6100000. ; C2- O2
5 6 2 0.10000 15700000. ; O2- HO2
1 2 2 0.14350 6100000. ; C1- O1
2 3 2 0.10000 15700000. ; O1- HO1

[ pairs ]
2 5 1 ; O1- O2
1 6 1 ; C1- HO2
4 3 1 ; C2- HO1

[ angles ]
; ai aj ak funct th0 cth
2 1 4 2 109.500 320.0000 ; O1- C1- C2
1 4 5 2 109.500 320.0000 ; C1- C2- O2
4 5 6 2 109.500 450.0000 ; C2- O2- HO2
1 2 3 2 109.500 450.0000 ; C1- O1- HO1

[ dihedrals ]
; ai aj ak al funct phi0 cp mult
2 1 4 5 1 0.000 2.530 3 ; dih
O1- C1- C2- O2
2 1 4 5 1 0.000 5.350 1 ; dih
O1- C1- C2- O2
1 4 5 6 1 0.000 1.260 3 ; dih
C1- C2- O2- HO2
4 1 2 3 1 0.000 1.260 3 ; dih
C2- C1- O1- HO1

; Include Position restraint file
; WARNING: Position restraints and distance restraints ought not be done
together
#ifdef POSRES
#include "posreethanediol.itp"
#endif

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; title from mol2 input
EDO_ideal.pdb

[ molecules ]
; molecule name nr.
EDO_ideal.pdb 1

===========ethanediol.top===========
Post by Nagy, Peter I.
It is extremely surprising that you have not found solute-solvent
hydrogen bonds in aqueous solution. What is the O-C-C-O conformation? If it
is trans, then what do the OH hydrogens do?
If O-C-C-O is gauche, then existence of two internal hydrogen bonds is possible, but it is
far from the quantum mechanically most stable form in the gas phase. I
think that at least one solute-solvent hydrogen bond should have been seen.
There are papers in the literature which do show solute-solvent hydrogen
bonds in water. The exciting question is: there is one
H-O-C-C trans moiety in the gas phase, and the other H is H-bonded to this
oxygen, when the O-C-C-O skeleton is gauche. Then the question of solvation
is, whether this intramolecular hydrogen bond is maintained or disrupts. In
aqueous solution it may, whereas in chloroform or CCl4 both OH may be
internally H-bonded. Experiments found 12% O-C-C-O trans and 88% O-C-C-O
gauche conformers in aqueous solution. Modeling should find what are the
positions of the hydroxy hydrogens.
If you really do not find solute-solvent hydrogen bonds, your
ethylene-glycol charges may be
questionable. What charge values did you use? A possibility is that the
glycol OH charges cannot compete with those of the water model (SPC, TIPxP
or what) in forming intermolecular hydrogen bonds.
Peter Nagy
The University of Toledo,
Toledo, OH 43606
-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Nancy
Sent: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation and
equilibration?
I am now trying to run MD on glycerol. I start with a "glycerol.mol2" file
which contains the structure of glycerol. I am using the following commands
$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6
I modified the "defaults" part of the "ffglycerol.itp" (generated by
===========================
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
===========================
$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p
glycerol.top -box 2.65 2.65 2.65
$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr
===========================
constraints = none
integrator = steep
nsteps = 10000
emtol = 10.0
emstep = 0.01
nstlist = 2
coulombtype = PME
nstcomm = 2
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
nstxout = 2
pbc = xyz
pme_order = 4
===========================
$ mdrun -v -deffnm em
===============================================================
Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5
Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4
Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4
Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4
Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
===========================
title = Glycerol NVT equilibration
define = -DPOSRES
integrator = md
nsteps = 5000
dt = 0.002
nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10
continuation = no
constraint_algorithm = lincs
constraints = all-angles
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = GOL SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
pbc = xyz
DispCorr = EnerPres
gen_vel = yes
gen_temp = 300
gen_seed = -1
===========================
where "GOL" refers to GlycerOL.
$ mdrun -v -deffnm nvt
When I execute the above command, I get numerous errors of the following
===============================================================
Step 0, time 0 (ps) LINCS WARNING
rms 0.326337, max 0.500490 (between atoms 1 and 3)
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'glycerol.pdb in water'
5000 steps, 10.0 ps.
Step 0, time 0 (ps) LINCS WARNING
rms 0.663850, max 1.227203 (between atoms 1 and 7)
atom 1 atom 2 angle previous, current, constraint length
1 3 172.3 0.2091 0.1644 0.2004
7 9 164.1 0.2082 0.1625 0.2004
2 3 124.5 0.1022 0.0787 0.1000
1 2 148.3 0.1477 0.0882 0.1435
5 6 30.4 0.0992 0.1265 0.1000
8 9 134.1 0.1014 0.0660 0.1000
7 8 138.2 0.1476 0.0991 0.1435
Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger
than the 1-4 table size 2.300 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
There were 12 inconsistent shifts. Check your topology
Segmentation fault
===============================================================
I don't know what is happening wrong. Please advise.
Thank you.
Nancy
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Justin A. Lemkul
2009-08-09 21:36:17 UTC
Permalink
Nancy wrote:

<snip>

Sounds like things are going fine.
Post by Nancy
I viewed the trajectory of the equilibration, and it looks reasonable.
The O-C-C-O conformation is mostly trans (anti) during the entire NVT
equilibration, and the OH hydrogens form numerous hydrogen bonds with
the solvent (it seems there are no intramolecular hydrogen bonds).
Therefore, the hydrogen bonds do form, given the charges adopted from
the methanol topology (O: -0.574, H: +0.398, CH2: +0.176). Do these
charge values seem reasonable?
"Reasonable" and "valid" are two separate ideas that may or may not be true
simultaneously. If you look, for example, at the charges on a serine side chain
in 53a6, all of your charges are very different. Since methanol was used to
parameterize serine, I don't know where the charges in the tutorial file came
from. The tutorial files claim to use 43a1, in any case, so be careful of
blindly copying parameters from some other location.

To convince a skeptical audience (i.e., reviewers) that your parameters are
valid, at least use the parameters from the functional groups present in the
force field parameter set you claim to be using. Beyond that, you should really
be validating the parameters based on the original force field methodology,
i.e., calculations of thermodynamic observables, described in full in the 2004
JCC paper dedicated to the 53a5 and 53a6 parameter sets.
Post by Nancy
The ethylene glycol lacks explicit non-polar hydrogens; is that normal
for this type of system, force field (based on GROMOS96 53a6) and SPC/E
water model?
Since G53a6 is a UA force field, by definition, yes. If this comes as a
surprise, you should certainly do a little background reading about this type of
force field and why you want to use it. Choosing a force field for simulation
is perhaps the most important part of running your experiments. If you don't
know the ins and outs (benefits, limitations, accuracy) of a particular
parameter set, you're asking for trouble if a reviewer asks you why you felt it
was best :)

-Justin
Post by Nancy
Thank you.
Nancy
===========ethanediol.top===========
;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "ffethanediol.itp"
[ moleculetype ]
; name nrexcl
EDO_ideal.pdb 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.00000 14.02700
; 0.0000000
2 OA 1 EDO O1 1 0.00000 15.99940
; 0.0000000
3 H 1 EDO HO1 1 0.00000 1.00800
; 0.0000000
4 CH2 1 EDO C2 2 0.00000 14.02700
; 0.0000000
5 OA 1 EDO O2 2 0.00000 15.99940
; 0.0000000
6 H 1 EDO HO2 2 0.00000 1.00800
; 0.0000000
; total molecule charge = 0.0000000
[ bonds ]
; ai aj funct b0 kb
1 4 2 0.15200 5430000. ; C1- C2
4 5 2 0.14350 6100000. ; C2- O2
5 6 2 0.10000 15700000. ; O2- HO2
1 2 2 0.14350 6100000. ; C1- O1
2 3 2 0.10000 15700000. ; O1- HO1
[ pairs ]
2 5 1 ; O1- O2
1 6 1 ; C1- HO2
4 3 1 ; C2- HO1
[ angles ]
; ai aj ak funct th0 cth
2 1 4 2 109.500 320.0000 ; O1- C1- C2
1 4 5 2 109.500 320.0000 ; C1- C2- O2
4 5 6 2 109.500 450.0000 ; C2- O2- HO2
1 2 3 2 109.500 450.0000 ; C1- O1- HO1
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
2 1 4 5 1 0.000 2.530 3 ;
dih O1- C1- C2- O2
2 1 4 5 1 0.000 5.350 1 ;
dih O1- C1- C2- O2
1 4 5 6 1 0.000 1.260 3 ;
dih C1- C2- O2- HO2
4 1 2 3 1 0.000 1.260 3 ;
dih C2- C1- O1- HO1
; Include Position restraint file
; WARNING: Position restraints and distance restraints ought not be done
together
#ifdef POSRES
#include "posreethanediol.itp"
#endif
; Include water topology
#include "spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; title from mol2 input
EDO_ideal.pdb
[ molecules ]
; molecule name nr.
EDO_ideal.pdb 1
===========ethanediol.top===========
On Sat, Aug 8, 2009 at 7:46 PM, Nagy, Peter I. <PNAGY at utnet.utoledo.edu
It is extremely surprising that you have not found solute-solvent
hydrogen bonds in aqueous solution. What is the O-C-C-O
conformation? If it is trans, then what do the OH hydrogens do?
If O-C-C-O is gauche, then existence of two internal hydrogen bonds
is possible, but it is
far from the quantum mechanically most stable form in the gas phase.
I think that at least one solute-solvent hydrogen bond should have
been seen. There are papers in the literature which do show
there is one
H-O-C-C trans moiety in the gas phase, and the other H is H-bonded
to this oxygen, when the O-C-C-O skeleton is gauche. Then the
question of solvation is, whether this intramolecular hydrogen bond
is maintained or disrupts. In aqueous solution it may, whereas in
chloroform or CCl4 both OH may be internally H-bonded. Experiments
found 12% O-C-C-O trans and 88% O-C-C-O gauche conformers in aqueous
solution. Modeling should find what are the positions of the hydroxy
hydrogens.
If you really do not find solute-solvent hydrogen bonds, your
ethylene-glycol charges may be
questionable. What charge values did you use? A possibility is that
the glycol OH charges cannot compete with those of the water model
(SPC, TIPxP or what) in forming intermolecular hydrogen bonds.
Peter Nagy
The University of Toledo,
Toledo, OH 43606
-----Original Message-----
From: gmx-users-bounces at gromacs.org
<mailto:gmx-users-bounces at gromacs.org> on behalf of Nancy
Sent: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation and
equilibration?
I am now trying to run MD on glycerol. I start with a
"glycerol.mol2" file
which contains the structure of glycerol. I am using the following commands
$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6
I modified the "defaults" part of the "ffglycerol.itp" (generated by
===========================
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
===========================
$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p
glycerol.top -box 2.65 2.65 2.65
$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr
===========================
constraints = none
integrator = steep
nsteps = 10000
emtol = 10.0
emstep = 0.01
nstlist = 2
coulombtype = PME
nstcomm = 2
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
nstxout = 2
pbc = xyz
pme_order = 4
===========================
$ mdrun -v -deffnm em
===============================================================
Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5
Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4
Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4
Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4
Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.3459230e+04
Maximum force = 4.9560604e+01 on atom 4
Norm of force = 3.4399371e+00
===============================================================
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
===========================
title = Glycerol NVT equilibration
define = -DPOSRES
integrator = md
nsteps = 5000
dt = 0.002
nstxout = 10
nstvout = 10
nstenergy = 10
nstlog = 10
continuation = no
constraint_algorithm = lincs
constraints = all-angles
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.3
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = GOL SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
pbc = xyz
DispCorr = EnerPres
gen_vel = yes
gen_temp = 300
gen_seed = -1
===========================
where "GOL" refers to GlycerOL.
$ mdrun -v -deffnm nvt
When I execute the above command, I get numerous errors of the following
===============================================================
Step 0, time 0 (ps) LINCS WARNING
rms 0.326337, max 0.500490 (between atoms 1 and 3)
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'glycerol.pdb in water'
5000 steps, 10.0 ps.
Step 0, time 0 (ps) LINCS WARNING
rms 0.663850, max 1.227203 (between atoms 1 and 7)
atom 1 atom 2 angle previous, current, constraint length
1 3 172.3 0.2091 0.1644 0.2004
7 9 164.1 0.2082 0.1625 0.2004
2 3 124.5 0.1022 0.0787 0.1000
1 2 148.3 0.1477 0.0882 0.1435
5 6 30.4 0.0992 0.1265 0.1000
8 9 134.1 0.1014 0.0660 0.1000
7 8 138.2 0.1476 0.0991 0.1435
Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger
than the 1-4 table size 2.300 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
There were 12 inconsistent shifts. Check your topology
Segmentation fault
===============================================================
I don't know what is happening wrong. Please advise.
Thank you.
Nancy
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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------------------------------------------------------------------------
_______________________________________________
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Nancy
2009-08-10 21:09:12 UTC
Permalink
The structure in the original PDB file of ethylene glycol was in the gauche
conformation. When I minimised the solvated system, the molecule remained
in the gauche conformation. However, during equilibration of the system,
the conformation of the molecule changed to trans within less than one
picosecond. It remained in the trans conformation for the rest of the
equilibration.


Thanks,
Nancy
Dear Nancy,
It was useful to find charges for the solute... I am not a GROMACS user,
so I do not know what checks have to be done for a non-protein or non-DNA
solute. Anyway, this case helped develop data management for a non-standard
solute.
It is normal to use united atom model for CH, CH2 and CH3 in GROMACS. As
far as the charges are concerned, it is always a matter of speculation.
Nobody knows what charges are "correct". Only a quantum MD (for the whole
system) helps, where you need not derive charges since you do not use
empirical pair potentials. Charges of -0.574 and 0.398 for the OH atoms are
reasonable, although somewhat larger absolute values could also be used.
Nonetheless, they already triggered the solute-solvent H-bonds, which was
the Nr. 1 problem.
I do not know what conformation you derived from the web. Was it
ORIGINALLY trans or gauche? As I wrote, the experiment found only 12% trans
in aqueous solution. Try to start the structure from the so-called tGg'
conformation or some other gauche(you may find them e.g. in our papers
JACS,1991, 113, 6719; 1992, 114, 4752 and a complete set of conformations in
the paper of Cramer and Truhlar in the JACS about 1995, I do not have the
reference handy). If the system stays in gauche, then the simulation has
been short starting from trans and/or the OCCO torsion barrier is too high
for equilibration. I would start from the tGg' and would conduct at least
500 ps long simulation, check if trans appears and what is the gauche/trans
ratio. If you do not find a trans starting from gauche or no gauche starting
from trans, then I would reduce the OCCO torisonal. Also check whether the
intramolcular hydrogen bonds remain maintained in the gauche structures.
Hopefully these above help.
The ratio is a sensitive problem, and could depend on the applied charge
sets, too. Thus you may need to conduct a more complicated test finding
combination(s) of charges and torsion parameters, which produce good
results. Maybe there are different combinations working equally well. I did
not meet this problem when I performed the free energy perturbation
calculations via Monte Carlo simulations with rigid solute geometries.
Best regards
Peter Nagy
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Bruce D. Ray
2009-08-10 22:22:28 UTC
Permalink
Post by Nancy
http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
Chimera (http://www.cgl.ucsf.edu/chimera/).
$ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir .../topolbuild1_2_2/dat/gromacs -ff gmx53a6
ethanediol.gro
ethanediol.log
ethanediolMOL.mol2
ethanediol.top
ffethanediol.itp
posreethanediol.itp
=======================================
#define _FF_GROMOS96
#define _FF_GROMOS53A6
#define _FF_USER
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
#include "ffG53a6nb.itp"
=======================================
The
lack of hydrogen bonds between the solute and solvent molecules was
Post by Nancy
due
to the lack of charges in the generated topology file
"ethanediol.top".
Post by Nancy
So I changed the "atoms" section of the topology
file (the original topology
Post by Nancy
file is at the end of this message), and
this causes hydrogen bonds between the
Post by Nancy
solute and solvent in numbers
comparable to that between the solvent molecules.
Post by Nancy
=======================================
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.17600 14.02700 ; 0.0000000
2 OA 1 EDO O1 1 -0.5740 15.99940 ; 0.0000000
3 H 1 EDO HO1 1 0.39800 1.00800 ; 0.0000000
4 CH2 1 EDO C2 2 0.17600 14.02700 ; 0.0000000
5 OA 1 EDO O2 2 -0.5740 15.99940 ; 0.0000000
6 H 1 EDO HO2 2 0.39800 1.00800 ; 0.0000000
; total molecule charge = 0.0000000
=======================================
I
obtained the charge values from the methanol tutoral included with
Gromacs
Post by Nancy
(.../share/gromacs/tutor/methanol/methanol.itp). I then
enlarge the box and solvate the molecule:

I used a mol2 file that I generated from a sy2 file downloaded from NCI by first
running the file through dos2unix then replacing the 0 in the residue number
column with 1 EDO so that I had both a correct residue number column with a
residue name column. The NCI data was missing the residue name column. I then
read the mol2 file that resulted into UCSF Chimera and used it to generate gasteiger
charges for ethylene glycol. Chimera wrote the following mol2 file as a result:

@<TRIPOS>MOLECULE
EDO
10 9 1 0 0
SMALL
AMBER99


@<TRIPOS>ATOM
1 O1 0.0000 0.0000 0.0000 O.3 1 EDO -0.3940
2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO 0.0662
3 C2 -1.7400 1.1400 -1.1400 C.3 1 EDO 0.0662
4 O2 -2.5200 1.2800 0.0200 O.3 1 EDO -0.3940
5 H1 0.5196 -0.8024 0.0879 H 1 EDO 0.2102
6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO 0.0588
7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO 0.0588
8 H4 -2.3721 1.1133 -2.0029 H 1 EDO 0.0588
9 H5 -1.0696 1.9696 -1.2252 H 1 EDO 0.0588
10 H6 -3.0271 2.0935 -0.0316 H 1 EDO 0.2102
@<TRIPOS>BOND
1 1 5 1
2 1 2 1
3 2 7 1
4 2 6 1
5 2 3 1
6 3 9 1
7 3 8 1
8 3 4 1
9 4 10 1
@<TRIPOS>SUBSTRUCTURE
1 EDO 2 RESIDUE 4 A EDO 0 ROOT


I processed this with topolbuild 1.3 and generated topologies with gromacs
53a6 and with opls-aa as the force fields. I am attaching the results to this
as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa atom
types selected by topolbuld 1.3 have characteristic atom type charges charges
of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,
+0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the
carbons. The comparison to the gasteiger charges Chimera assigned to these
atoms is interesting. The opls-aa topology generated also assigns to the
O1-C1-C2-O2 dihedral the diol constants found as a special define in
ffoplsaabon.itp

{snipped}
Post by Nancy
The ethylene glycol lacks explicit non-polar hydrogens; is that
normal for this type of system,
Post by Nancy
force field (based on GROMOS96 53a6)
and SPC/E water model?

The 53a6 force field is a united atoms model force field and incorporates non-polar
hydrogens in the parameters of the carbons to which they are bound. If you want
to treat the non-polar hydrogens separately from the carbons to which they are
bound, you will need to use an all atoms force field such as opls-aa for which I
have included the parameters in the attached tarred and gzipped file, ethanediol.tgz

I hope this is useful.
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273




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Nancy
2009-08-13 00:47:33 UTC
Permalink
Hello,

In an earlier message, it was stated that topolbuild generated topologies
with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version
1.2.2), and the only files in the "dat/gromacs" directory are for the force
fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-AA force
field used?

Thank you.

Nancy
Post by Nancy
Post by Nancy
http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
Chimera (http://www.cgl.ucsf.edu/chimera/).
I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the
$ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir
.../topolbuild1_2_2/dat/gromacs -ff gmx53a6
Post by Nancy
ethanediol.gro
ethanediol.log
ethanediolMOL.mol2
ethanediol.top
ffethanediol.itp
posreethanediol.itp
=======================================
#define _FF_GROMOS96
#define _FF_GROMOS53A6
#define _FF_USER
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
#include "ffG53a6nb.itp"
=======================================
The lack of hydrogen bonds between the solute and solvent molecules was
due to the lack of charges in the generated topology file
"ethanediol.top".
Post by Nancy
So I changed the "atoms" section of the topology file (the original
topology
Post by Nancy
file is at the end of this message), and this causes hydrogen bonds
between the
Post by Nancy
solute and solvent in numbers comparable to that between the solvent
molecules.
Post by Nancy
=======================================
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.17600 14.02700
; 0.0000000
Post by Nancy
2 OA 1 EDO O1 1 -0.5740 15.99940
; 0.0000000
Post by Nancy
3 H 1 EDO HO1 1 0.39800 1.00800
; 0.0000000
Post by Nancy
4 CH2 1 EDO C2 2 0.17600 14.02700
; 0.0000000
Post by Nancy
5 OA 1 EDO O2 2 -0.5740 15.99940
; 0.0000000
Post by Nancy
6 H 1 EDO HO2 2 0.39800 1.00800
; 0.0000000
Post by Nancy
; total molecule charge = 0.0000000
=======================================
I obtained the charge values from the methanol tutoral included with
Gromacs
Post by Nancy
(.../share/gromacs/tutor/methanol/methanol.itp). I then enlarge the
I used a mol2 file that I generated from a sy2 file downloaded from NCI by first
running the file through dos2unix then replacing the 0 in the residue number
column with 1 EDO so that I had both a correct residue number column with a
residue name column. The NCI data was missing the residue name column. I then
read the mol2 file that resulted into UCSF Chimera and used it to generate gasteiger
@<TRIPOS>MOLECULE
EDO
10 9 1 0 0
SMALL
AMBER99
@<TRIPOS>ATOM
1 O1 0.0000 0.0000 0.0000 O.3 1 EDO
-0.3940
2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO
0.0662
3 C2 -1.7400 1.1400 -1.1400 C.3 1 EDO
0.0662
4 O2 -2.5200 1.2800 0.0200 O.3 1 EDO
-0.3940
5 H1 0.5196 -0.8024 0.0879 H 1 EDO
0.2102
6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO
0.0588
7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO
0.0588
8 H4 -2.3721 1.1133 -2.0029 H 1 EDO
0.0588
9 H5 -1.0696 1.9696 -1.2252 H 1 EDO
0.0588
10 H6 -3.0271 2.0935 -0.0316 H 1 EDO
0.2102
@<TRIPOS>BOND
1 1 5 1
2 1 2 1
3 2 7 1
4 2 6 1
5 2 3 1
6 3 9 1
7 3 8 1
8 3 4 1
9 4 10 1
@<TRIPOS>SUBSTRUCTURE
1 EDO 2 RESIDUE 4 A EDO 0 ROOT
I processed this with topolbuild 1.3 and generated topologies with gromacs
53a6 and with opls-aa as the force fields. I am attaching the results to this
as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa atom
types selected by topolbuld 1.3 have characteristic atom type charges charges
of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,
+0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the
carbons. The comparison to the gasteiger charges Chimera assigned to these
atoms is interesting. The opls-aa topology generated also assigns to the
O1-C1-C2-O2 dihedral the diol constants found as a special define in
ffoplsaabon.itp
{snipped}
Post by Nancy
The ethylene glycol lacks explicit non-polar hydrogens; is that normal
for this type of system,
Post by Nancy
force field (based on GROMOS96 53a6) and SPC/E water model?
The 53a6 force field is a united atoms model force field and incorporates non-polar
hydrogens in the parameters of the carbons to which they are bound. If you want
to treat the non-polar hydrogens separately from the carbons to which they are
bound, you will need to use an all atoms force field such as opls-aa for which I
have included the parameters in the attached tarred and gzipped file, ethanediol.tgz
I hope this is useful.
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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Bruce D. Ray
2009-08-13 11:42:57 UTC
Permalink
Post by Nancy
In an earlier message, it was stated that topolbuild generated
topologies with Gromos 53a6
Post by Nancy
and OPLS-AA force fields. I am using
topolbuild (version 1.2.2), and the only files in the
Post by Nancy
"dat/gromacs"
directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and
53a6.
Post by Nancy
How is the OPLS-AA force field used?
First, I need to thank you in particular. First, while testing your molecules, I discovered a
case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed
to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as
the force field. Second, also because of this, I discovered what one downloads as a "Sybyl
2" structure from one source of small molecule structures and how to edit it so that it meets
the syntax standards for a true mol2 file. Thank you very much for this assistance.

In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) generates topologies for
amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and
53a6. I stated that the as yet
unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have,
is 1.2.2. Would you like to beta test topolbuild 1.3?


Sincerely,

--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273




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Nancy
2009-08-13 23:15:33 UTC
Permalink
I'm glad to be of help; yes, I would like to beta test topolbuild 1.3.

Thank you.
Post by Nancy
Post by Nancy
In an earlier message, it was stated that topolbuild generated topologies
with Gromos 53a6
Post by Nancy
and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the
only files in the
Post by Nancy
"dat/gromacs" directory are for the force fields: 43a1, 43a2, 43b1, 45a3,
53a5, and 53a6.
Post by Nancy
How is the OPLS-AA force field used?
First, I need to thank you in particular. First, while testing your
molecules, I discovered a
case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed
to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as
the force field. Second, also because of this, I discovered what one downloads as a "Sybyl
2" structure from one source of small molecule structures and how to edit
it so that it meets
the syntax standards for a true mol2 file. Thank you very much for this assistance.
In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2)
generates topologies for
amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. I stated that
the as yet
unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have,
is 1.2.2. Would you like to beta test topolbuild 1.3?
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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Dallas B. Warren
2009-08-11 01:34:11 UTC
Permalink
You might want to consider the parameters I developed for propylene
glycol .... http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms of the parameterisation of ethylene glycol.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
Nancy
2009-08-11 11:40:08 UTC
Permalink
Thank you for the article.

Nancy


On Mon, Aug 10, 2009 at 9:34 PM, Dallas B. Warren <
Post by Dallas B. Warren
You might want to consider the parameters I developed for propylene
glycol .... http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms of the parameterisation of ethylene glycol.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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