VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Aug 20 2015 - 10:37:12 CDT

Hi!

(Very) large pressure fluctuations are expected
<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/3864.html>.
What value do you get if you average over the whole trajectory?

Regards,
Ajasja

On 20 August 2015 at 15:54, Daniela Rivas <dani.rivas.r_at_gmail.com> wrote:

> Hi,
>
> I have a question about the Namd Plot Plugin. When I select to plot the
> Pressure, what exactly does it plot? I'm getting really high pressures
> (around 2.000 bar) and it doesn't make sense to me.
>
> My Namd log file is from a Molecular Dynamics simulation of a membrane
> protein (150.000 atoms in the system app.). I set the pressure at 1 atm but
> also used the *useGroupPressure.*
>
> Thanks in advance,
> Daniela.
>