you would need to write some code to do it.
do you know fortran?
On 10/4/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> Dear All,
>
> I am trying to run MD using multi chain system in implicit solvent by
> setting up a box using setBox command in leap, but generalized born
> simulations can only be run for non-periodic systems, so the chains are
> diffusing away from each other during the simulation run.
> I want to create an imginary sphere around the molecule and if the
> distance of atom from the center of mass is longer than the length of the
> imaginary sphere, then, i want to apply additional force imposed on that
> atom (the direction is to the center of mass).
> What options can I use to keep the chains in a box (not flying far away
> from each other) whose sphere I am specifying.
> Any suggestions how to do it in amber9
>
>
> Regards
> priya
>
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Received on Sun Oct 07 2007 - 06:07:24 PDT
