[gmx-users] pressure coupling

[Mohsen Ramezanpour]

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.

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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