RE: AMBER: How to do minimization..

From: Ross Walker <>
Date: Mon, 8 Jan 2007 08:32:09 -0800

Dear Vikram,
The answers to your questions and many more are available through the Amber
Make sure you work through these first which will explain things like how to
do minimization.
With regards to your specific questions I will assume that you have
successfully built this system with the necessary parameters.
I would start by just minimizing everything and see if it works, chances are
you will be good. If you come across problems then try restraining the
surfactants and any other solutes weakly in the first step of minimization
and then release these restraints in the second step. As to restraining the
surfactants during MD this is really something you just need to test. First
of all try doing the heating and equilibration without restraints and see
what happens. Then if need be you can repeat it in two stages, a first stage
with weak restraints and then a second stage where you equilibrate without
the restraints.
With regards to how long to equilibrate for you can obtain this sort of
information by looking at energy vs time plots, rmsd's etc. Working through
the tutorials will show you this sort of procedure.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: [] On Behalf Of
sai vikram
Sent: Monday, January 08, 2007 07:31
Subject: AMBER: How to do minimization..

Hi all,

It is a basic question.

I am doing simulation of a system. which is having organic solvent,
surfactant and water .

How can i do minimization?

How to treat water in the system?

Is it necessary to do with restrain, on surfactants at first and later with

How could i know the relaxation time of an organic solvent?

Can someone please advice me here.

Thanks in advance


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Received on Wed Jan 10 2007 - 06:07:25 PST
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