[gmx-users] Fatal Equilibration Errors

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 8 21:49:19 CEST 2009

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.


> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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