From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 18 2007 - 14:23:07 CDT
it would help if you clarify what you expect somewhat. If you're running
NVT/NPT, total energy of your system is *not* conserved (see definition
of these ensembles). Because the extended system is just a clone of your
direct system, though, if an ensemble is being enforced on your unit
cell, it applies to the periodic system as well (since they're the same ;-).
> Searching through the NAMD documentation and the mailing list, I've been
> unable to find where I would look to make sure that energy conservation is
> being enforced in the extended system when using either a thermo- or
> barostat for NVT or NPT simulations. My understanding is that TOTAL,
> TOTAL2 and TOTAL3 are only telling you about the sum of the PE and KE for
> the direct system.
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