Re: [AMBER-Developers] [AMBER] manual prmtop file editing for free energy calculation

From: Jason Swails <>
Date: Mon, 28 May 2012 15:16:33 +1000

On May 28, 2012, at 10:31 AM, Thomas Cheatham <> wrote:

>> This also means, incidentally, that the OPLS force field is not properly
>> supported by pmemd.cuda since the original NB coefficients are
>> de-combined and re-combined using the Amber combining rules. This was a
>> relatively recent discovery of ours which I haven't gotten a chance to
>> really pursue.
> It also means that NBFIX will not work correctly, i.e. CHARMM ion
> parameters, etc. People could convert over PSF's and not get the same
> results when running on GPUs. I notice now that the DHFR test case in
> test/chamber/md_engine gives slightly different VDW with pmemd.cuda vs.
> pmemd or sander... --tom

NBFIX can be hacked into the prmtop file using parmed, but there is no other way of doing it, as Ross mentioned.

And you are correct--pmemd.cuda will not support it.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sun May 27 2012 - 22:30:03 PDT
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