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 - 07:30:04 PDT
