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

From: Ross Walker <>
Date: Sun, 28 Jan 2007 22:16:32 -0800

Dear Jiapu,
Can you post the input files for phase I and II? Are you definately
restarting phase II from phase I? I.e. set irest=1 and ntx=5? Otherwise you
will get velocities reset and this will likely give you a jump in kinetic
energy which quickly feeds into potential energy and could manifest itself
as a small jump in RMSD.
All the best

|\oss Walker

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From: [] On Behalf Of
Sent: Sunday, January 28, 2007 22:05
Subject: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1

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,


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Received on Wed Jan 31 2007 - 06:07:18 PST
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