From: Jacob Poehlsgaard (mail_lists_at_hardcoil.net)
Date: Wed Sep 20 2006 - 04:54:37 CDT
I'm still wrestling with understanding all aspects of NAMD and didn't
realize that xsc files override the cell vector settings. It's working now,
with switching off the control after 500 ps.
With regards to running in NVE: My preference comes from the papers I've
been reading, stating that the actual production run should be in that
ensemble. I must admit I do not quite understand why this is, unless setting
temperature and pressure is somehow "cheating" or preventing the system from
acting naturally. Has the consensus on this changed, or am I reading the
wrong papers/list entries?
Jim Phillips wrote:
> You need to equilibrate periodic simulations with constant
> pressure to prevent bubbles from forming (or over-compressing
> the system). Be sure to use the extendedSystem option to
> read the modified basis vectors from the .xsc file when
> restarting a run. Once you've equilibrated both pressure and
> temperature you can switch to NVE if that's necessary for some reason.
Cesar Luis Avila wrote:
> What's the problem on running production simulation on NPT ensemble?
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