[gmx-users] Re: Running Pull Code

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri May 17 13:16:06 CEST 2013

Thanks for your reply.
It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. 

I appreciate your suggestion.


----- Original Message -----
From: Thomas Schlesier <schlesi at uni-mainz.de>
To: gmx-users at gromacs.org
Sent: Friday, May 17, 2013 3:30 PM
Subject: [gmx-users] Re: Running Pull Code

The three steps (EM, NVT and NPT) are to equilibrate the system. How 
much time these steps need depends on the system. But i would assume a 
ouple of nanosecounds are sufficient for most systems. You could look 
into the literature, how long other people equilibrate systems which are 
similar to ours.
If the system is equilibrated, you an start to perform the pulling 
simulation to obtain the individual structure for the later umbrella 


Am 17.05.2013 07:46, schrieb gmx-users-request at gromacs.org:
> Hi,
> I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling.
> I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT?
> As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well?
> Would you please give me any suggestions?
> Thanks in advance.
> Sincerely,
> Shima?

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