[gmx-users] Fatal Equilibration Errors
Nancy
nancy5villa at gmail.com
Sat Aug 8 23:46:30 CEST 2009
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==========
On Sat, Aug 8, 2009 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Nancy wrote:
>
>> 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
>> 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
>
>
>> Nancy
>>
>>
>>
>>
>> On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Nancy wrote:
>>
>> 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
>> ===============================================================
>>
>> As I believe these forces to be acceptable, I proceed to
>> equilibration:
>>
>>
>> These values appear to be reasonable, yes.
>>
>>
>> $ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr
>>
>> where my "nvt.mdp" file is:
>>
>>
>> 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
>> appropriate. See here:
>>
>> 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
>>
>> ========================================
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>
> --
> ========================================
>
> 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!
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