Dear Simmerling,
Thanks for your reply.
By drifting I mean the system as a whole has a
movement
in a direction during the heating from 293K to 300 at
constant pressure. (I think the center of mass has a
velocity in a particular direction). After 10ps, the
system attains 300K and after that there is no such
movement.
--- Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
wrote:
> what do you mean by the "nucleic acid is drifted"?
> you'll need to be much more specific. Also check the
> archives and read the manual about imaging in case
> that
> is the problem.
>
> mathew k varghese wrote:
>
> >Dear AMBER users,
> >
> >
> >I am runnig MD simulation of a nucleic acid in
> >explicit solvent. In the first step of
> equillibration
> >the system is heated to 300K(actual final
> temperature
> >attained is 293.18K)at constant VOLUME in 50ps. In
> the
> >next step the run was in constant PRESSURE and I
> >heated the system in 10ps from 293.18 to 300 and
> then
> >40ps at 300 k.
> >When the trajectory is viewed, during the 10ps
> heating
> >from 293.18 to 300 at constant pressure the nucleic
> >acid is drifted. Is it normal? If not how can I
> >correct this?
> >
> >
>
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/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
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Received on Fri Sep 09 2005 - 14:53:00 PDT
