AMBER Archive (2007)

Subject: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1

From: Jiapu.Zhang_at_csiro.au
Date: Mon Jan 29 2007 - 00:04:34 CST

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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