[gmx-users] water box with prescribed volume and density

grivet grivet at cnrs-orleans.fr
Thu Apr 1 16:15:30 CEST 2010

Le mardi 30 mars 2010 à 12:26 -0400, Justin A. Lemkul a écrit :
> > 
> > Having cleared the first hurdle, I ran mdrun for steepest descent (5832
> > molecules). The program stopped after 2067 steps, with maximum force =
> > 1.58E02 on atom 4870. How important is that warning?
> > 
> What warning?  This one?
> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

I wanted to know what maximum force was acceptable at this stage of the

> > The volume and density evolved rather smoothly to reasonable values. I
> > have two values for the density; according to the .log file, it is
> > 0.9937E03 and according to g_energy, it is 1.015E03; which should I
> > believe?
> > 
> Probably g_energy.  See the manual, Appendix C.  How many values in the .log 
> file are you looking at?  Anything printed there is just an instantaneous value, 
> and may not represent the actual average over the simulation.

You're right; both give identical averages.

rlist, rcoulomb and rvdw were all set to 1.0; is that reasonable ?

Thank you for your time and help
JP Grivet

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