cellBasisvectors/.xsc fixing/colvars while running amber ff

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 21 2011 - 13:13:57 CDT

I am running parm7 amber files with namd 2.8 cuda for a protein
complex in a rectangular box, TIP3PBOX water. After heating to 310K,
at the first pressure equilibration with protein complex atoms fixed,
and commented out cellBasisvectors ( xsc file specified), I notice
unusually many water molecules out of the box. Only 25,000 steps,
timestep 1fs, were carried out.

Question: should, when running amber ff, the cellBasisVectors be
always specified? Is the answer the same when colvars are applied in
place of fixing atoms?

francesco pietra

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