From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Feb 20 2013 - 04:29:50 CST
Salut FX,
----- 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
> beforehand.
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.
Cheers,
Jérôme
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