Batch Mode MD simulation Script for NAMD

From: Babban Mia (
Date: Thu Aug 11 2011 - 18:56:19 CDT

Hello Everyone

I am setting up a en explicit solvent MD simulation for 100ns and I want to
save my structure at every 1ps thus giving me about 100000 structures [PDB
files] of my protein.

I will be very grateful if someone could give me/share the batch mode[shell]
with a corresponding config file for a periodic boundary explicit MD
simulation .I am sure lot of people would have used NAMD in a batch mode and
it will be a good starting point to make a batch mode script for my

Much like CHARMM,I guess I would have to first store the .res file for every
1 ps of MD simulation which could then be converted to a PDB file.

Thanks again!

Best regards

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:34 CST