[gmx-users] Fatal Equilibration Errors

[Justin A. Lemkul]

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

========================================