this is one of the main problems of shell models. Have you read what others
have
done in that area? We reviewed these in last year's issue of the ACS Annual
Report in Computational Chemistry (Okur and Simmerling).
you would probably be better off changing the code to reverse your water
direction
during MD rather than from the restart file. Of course this will change the
system dynamics.
On 2/15/07, Ji-Lai Li <jlutcc.gmail.com> wrote:
>
> Dear Amber Users:
> I am doing targeted md. My protein is solvated by a shell of water. The
> whole has been equilibrated. When the TMD runs for a period of time,
> sometimes 300 ps, or 500ps, there is a water molecule escapes from the
> surface. It is headachy.
> Now, I want to modify the velocity of the escaping water, and let it run
> to the opposite direction. I think it is physical. Correct? If yes, how to
> modify it form the *.rst file?
> Is there someone know the realy meaning of the RST file?
>
> Ji-Lai Li
>
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Received on Sun Feb 18 2007 - 06:07:27 PST
