AMBER Archive (2005)

Subject: Re: AMBER: Equillibration run

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Sep 09 2005 - 06:16:55 CDT

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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