Re: protocol to start MD

From: Rabab Toubar (
Date: Wed Aug 19 2009 - 11:04:12 CDT

Hi Jose,

Have you tried to look at the namd tutorial...the basic steps is covered there

Rabab Toubar

--- On Wed, 8/19/09, jose correa <> wrote:

From: jose correa <>
Subject: namd-l: protocol to start MD
To: "namd-l" <>
Date: Wednesday, August 19, 2009, 10:27 AM

Dear all I want to ask you about the protocol to star MD step by step: 1.- obtain the 3-D of protein (from pdb ect) 2.- clean it from water, ligands etc. 3.- minimization in vacuo 4.- solvate and ionize 5.- minimized water and ions freezing the protein 5.- MD of water and ions freezing the protein 6.- minimizing the whole system 7.- heating (MD) from 10 to 310 K 8.- Run a short MD under NTP 9.- Run the MD (large) under NTV Is it ok?,  could you suggest me any reference?. Best wishes José Correa-Basurto ESM-IPN, mexico
  __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:12 CST