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
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk <
http://www.rosswalker.co.uk/> | PGP Key
available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Jiapu.Zhang.csiro.au
Sent: Sunday, January 28, 2007 22:05
To: amber.scripps.edu
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,
Jiapu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 31 2007 - 06:07:18 PST
