[gmx-users] Fatal Equilibration Errors
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 8 21:49:19 CEST 2009
> 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.
> 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:
> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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