VMD-L Mailing List

From: Dani (dani.rivas.r_at_gmail.com)
Date: Thu Aug 20 2015 - 13:27:57 CDT

Thanks a lot! That worked out perfectly. Now the pressure fluctuates between -20 and 20 bar and makes a lot more sense :)

Daniela.

> El 20-08-2015, a las 15:26, Dani <dani.rivas.r_at_gmail.com> escribió:
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>> El 20-08-2015, a las 14:35, Richard Wood <Richard.Wood_at_purduecal.edu> escribió:
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>> 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.
>>