AMBER: Molecular dynamic issues

From: Sophie Barbe <>
Date: Tue, 23 Jan 2007 15:34:50 +0100


I have several questions about the molecular dynamic methods for the proteins.

1- When we perform a simulation in explicit solvent, is it better to keep
crystallographic waters or to remove them ?

2- Is it better to use a cubic or an octahedral box to simulate the dynamic of a
protein in solution?

3- Is it possible to simulate a molecular dynamic simulation of a protein in
implicit solvent (using the generalized born model) in keeping
the crystallographic waters?

Thank you very much for your help

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Received on Wed Jan 24 2007 - 06:07:37 PST
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