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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 24 2007 - 06:07:37 PST
