[gmx-users] Fatal Equilibration Errors

[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?

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



On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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