[gmx-users] System equilibrium problems

[Parker de Waal]

Hi Mark,

Thanks for your response,

Currently I'm using the gromos53a6 force field because it is compatible
with heme cofactor found within P450.
I'll look through the literature again to double check my settings for my
NvT, NpT and energy minimization steps
as well, however any further insight would be greatly appreciated!

Parker


On Fri, Jun 14, 2013 at 4:13 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
> <Parker.deWaal09 at kzoo.edu>wrote:
>
> > Hi everyone,
> >
> > I recently tried to perform an 25 ns simulation on 12 nodes and was
> greeted
> > with this error around 3.2 ns into the run.
> >
> > '3 particles communicated to PME node 9 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> y.'
> >
> > To my knowledge the system has reached equilibrium as shown by energy
> > minimization, nvt and npt runs prior to the md run. The only thing that
> > concerns me is the Pressure average of 1.9
> >
>
> This is normal, see
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
>
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> >
> >
> -------------------------------------------------------------------------------
> > Potential                   -921529      32000    94074.9    -214425
> >  (kJ/mol)
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> >
> >
> -------------------------------------------------------------------------------
> > Temperature                 300.033       0.16    1.57434  -0.790469  (K)
> >
> > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> >
> >
> -------------------------------------------------------------------------------
> > Pressure                    1.94649       0.32    91.4545    1.28586
>  (bar)
> > Density                     1012.96      0.037   0.778484 -0.0126246
> >  (kg/m^3)
> >
> > Additionally here is a link to my md.mdp file
> >
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh
>
>
> Seems fine, apart from fourierspacing being rather more lax than normal. Be
> sure your settings are compatible with those used for your force field.
>
> Mark
>
>
> >
> >
> > Any input would be greatly appreciated!
> > Parker
> > --
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