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

From: Thomas Cheatham <>
Date: Sun, 27 May 2012 18:31:55 -0600 (Mountain Daylight Time)

> 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

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Received on Sun May 27 2012 - 18:00:03 PDT
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