Thanks Jason
On Tue, Aug 12, 2014 at 4:17 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Aug 12, 2014 at 10:09 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
>
> > Hi,
> > I checked that ibelly is not applicable with PMEMD so in order to put
> > restrain on my protein during minimization and heating, I am using
> > sander.MPI ..
> >
> > And once it is equilibrated, I used PMEMD.cuda to run the actually
> > production. Is it acceptable ?
> >
>
> Yes.
>
> As a side note, you can often use positional restraints instead of belly to
> keep atoms fixed to a certain spot with a spring constant while still
> allowing it to jiggle a _little_. This is more common in my experience
> than using belly, but YMMV.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Aug 12 2014 - 08:00:02 PDT
