[gmx-users] Running Pull Code

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri May 17 05:58:11 CEST 2013


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.

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