AMBER Archive (2007)

Subject: Re: AMBER: How to perform MD simulation in NVT ensemble?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Aug 24 2007 - 21:21:59 CDT

On 8/23/07, WANG,YING <wangying_at_ufl.edu> wrote:
> Hi, GREAT Thanks!!
> And I have an additional question........... :) Could I give an
> initial velocity of some of the atoms of a protein? Change the
> .inpcrd file? And I want to keep this velocity during the whole
> NVT simulation process, at the same time, I let the other atoms of
> this protein move freely. Is it possible?
> Sorry for so many questions................... Thanks very much!!
> Thanks the amber community!

Give an initial velocity is possible - all you need to do is to change
the restart file by hand. (Look into
http://amber.scripps.edu/formats.html#restart for details).

As far as keeping the velocity fixed during the simulation, I don't
think it is possible without changing the code, but I hope others will
correct me if I'm wrong.

Gustavo.
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