Re: protocol to start MD

From: Rabab Toubar (rtoubar_at_yahoo.com)
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
Regards

Rabab Toubar

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

From: jose correa <corrjose_at_gmail.com>
Subject: namd-l: protocol to start MD
To: "namd-l" <namd-l_at_ks.uiuc.edu>
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
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