Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ??

From: Jason Swails <>
Date: Tue, 12 Aug 2014 10:17:48 -0400

On Tue, Aug 12, 2014 at 10:09 AM, Hirdesh Kumar <>

> 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 ?


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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 12 2014 - 07:30:04 PDT
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