From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Feb 20 2013 - 04:29:50 CST
----- Original Message -----
> 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
To the best of my knowledge, NAMD only minimizes at constant volume. The minimizer might blow up for various reasons, but nothing should happen to the unit cell - if it does, then maybe you have unintentionally started an MD run.
AFAIK, all barostat (and thermostat) settings are just ignored until some form of MD starts.
> 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?
There isn't. That's certainly something you'd expect from a solid-oriented code, but in NAMD (and other similar programs), you'll have to do it more or less manually.
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