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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