VMD-L Mailing List

From: Dani (dani.rivas.r_at_gmail.com)
Date: Thu Aug 20 2015 - 13:26:33 CDT

> El 20-08-2015, a las 14:35, Richard Wood <Richard.Wood_at_purduecal.edu> escribió:
>
> If one computes the running average pressure, its value will approach the target value the longer the simulation runs.
>
> Richard
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Ajasja Ljubetič [ajasja.ljubetic_at_gmail.com]
> Sent: Thursday, August 20, 2015 10:37 AM
> To: Daniela Rivas
> Cc: Vmd l
> Subject: Re: vmd-l: Namd Plot Plugin
>
> Hi!
>
> (Very) large pressure fluctuations are expected. 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.
>