Constant volume energy minimization

From: FX (
Date: Tue Feb 19 2013 - 16:06:53 CST

Hi all,

(I am new to NAMD, though I have performed plenty of MD and MC with other tools before). Two quick questions I couldn't find the answer in the documentation:

  1. How can I run a constant-volume energy minimization? I have a periodic system (cubic), and energy minimization at constant pressure (which appears to be the default) just makes my unit cell implode. I'd like to run a short minimization with fixed unit cell beforehand.

  2. How do I build a supercell of a given size? I sure can duplicate pdb/psf files on my own, and simply feed them to NAMD, but there probably is a "built in" way of doing that at the start of the simulation in NAMD, isn't there?

Many thanks in advance, and sorry I couldn't find the above answers either in the documentation and the mailing-list (I promise, I looked!).


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