protocol to start MD

From: jose correa (
Date: Wed Aug 19 2009 - 09:27:29 CDT

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
Josť Correa-Basurto
ESM-IPN, mexico

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