From: Michael Mazack (michael_at_mazack.org)
Date: Tue Feb 19 2013 - 16:18:00 CST
Though I'm not sure about your second question, the answer to your first
question seems to be in your attached input file. The input file seems to
be using the Langevin piston barostat, which will resize the simulation
box. In NAMD, the barostat is off by default, so commenting out all of
those LangevinPiston-type lines or setting "LangevinPiston off" should
force the unit cell volume to remain constant. It also appears that
"minimize 100" is commented-out.
Hope that helps.
On Tue, Feb 19, 2013 at 4:06 PM, FX <fxcoudert_at_gmail.com> wrote:
> 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
> 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!).
-- Michael J. M. Mazack Scientific Computation Program University of Minnesota Minneapolis, MN 55455 E-mail: michael_at_mazack.org Web: http://mazack.org
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