[gmx-users] Fatal Equilibration Errors
nancy5villa at gmail.com
Sat Aug 8 22:45:25 CEST 2009
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?
On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Nancy wrote:
>> 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
> 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
>> 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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