Dear Amber friends,
Recently when I do equilibration, first the system was warmed up from
tempi to temp0, using ntt=3. I call it phase I. Then I want to do
further equilibration at temp0 (constant temperature now), during which
I still use ntt=3 (or use ntt=1). I call it phase II. All these two
phases are done under constant volume (i.e. ntb=1). However, when I draw
the RMSD-time graph of phase I and phase II, I always see there is a
gap, about 0.1 angstroms, between the RMSD of phase I and the RMSD of
phase II. This is not wanted by my theoretical think. Could someone
explain me why there is such a ugly jump for the RMSD? Thanks in
advance.
Sincerely yours,
Jiapu
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Received on Wed Jan 31 2007 - 06:07:17 PST
