AMBER Archive (2007)

Subject: AMBER: Molecular dynamic issues

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Tue Jan 23 2007 - 08:34:50 CST

Hi,

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

Sophie
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