AMBER Archive (2008)

Subject: AMBER: initial velocities of MD

From: Jena M (jeninhas_at_hotmail.com)
Date: Tue May 13 2008 - 11:37:31 CDT

 
Hi,
 
I have run a MD simulation of a protein and the trajectory revealed instabilities in some regions of that protein. So I would like to ran the MD simulation again but using different initial velocities, in order to see if I these instabilities are kept. Does anyone know how to change the initial velocities? Can I use the same top and crd files to initiate the equilibration phase?
 
Thanks a lot,
Jena
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