it's not really practical without knowing fortran or
finding someone at your institution that can help you.
I can tell you what to do in general terms but someone
needs to write the code and test it. I suggest cheching
for people locally and let us know if you can find a
colleague that is experienced with programming and
can help you.
On 10/4/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
>
> Dear Sir,
>
> I dont know much fortran.
> BUt some suggestions for the changes would help me to do that.
>
> priya
>
> *Carlos Simmerling <carlos.simmerling.gmail.com>* wrote:
>
> 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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>
>
>
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Received on Sun Oct 07 2007 - 06:07:24 PDT
