[gmx-users] pressure coupling

[Mark Abraham]

On Tue, Nov 19, 2013 at 8:07 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi
>
> I think the most important is the average of pressure not the
> pressure fluctuations!
> I think you should check the averaged pressure than the pressure to be
> constant at the desired pressure.
>

Yes, and bear in mind
http://www.gromacs.org/Documentation/Terminology/Pressure and that the
warning advised you to equilibrate *first* with Berendsen...

Mark


> Best
> Mohsen
>
>
> On Tue, Nov 19, 2013 at 10:11 PM, kiana moghaddam <ki_moghaddam at yahoo.com
> >wrote:
>
> > Dear GMX Users
> >
> > I have encountered with the following warning during NPT simulation of
> > DNA-ligand interaction by Parrinello-Rahman pressure coupling (ref_p:
> 1bar).
> >
> > WARNING 1:
> >
> > You are generating velocities so I am assuming you are equilibrating
> > a system. You are using Parrinello-Rahman pressure coupling, but this
> > can be unstable for equilibration. If your system crashes, try
> > equilibrating first with Berendsen pressure coupling. If you are not
> > equilibrating the   system, you can probably ignore this warning.
> >
> > After that, I used Berendsen pressure coupling without any warning.
> > Pressure fluctuations were between -1000-1000 bar. There are 730 atoms
> and
> > 13071 waters in my system.
> > Although I didn't get any warning, I'm not sure that
> > the Berendsen coupling and Pressure fluctuations for this system is
> correct?
> >
> > Please help me
> >
> > Best Regards
> > kiana
> > --
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