From: Richard Wood (
Date: Thu Aug 20 2015 - 12:35:54 CDT

If one computes the running average pressure, its value will approach the target value the longer the simulation runs.

From: [] on behalf of Ajasja Ljubetiè []
Sent: Thursday, August 20, 2015 10:37 AM
To: Daniela Rivas
Cc: Vmd l
Subject: Re: vmd-l: Namd Plot Plugin


(Very) large pressure fluctuations are expected<>. What value do you get if you average over the whole trajectory?


On 20 August 2015 at 15:54, Daniela Rivas <<>> wrote:

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,