[gmx-users] Re: Running Pull Code

[Thomas Schlesier]

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 
sampling.

Greetings
Thomas

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?