AMBER: Equillibration run

From: mathew k varghese <>
Date: Fri, 9 Sep 2005 07:40:08 +0100 (BST)

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?

 Thanks in advance for any help



Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



Yahoo! India Matrimony: Find your partner now. Go to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Sep 09 2005 - 07:53:01 PDT
Custom Search