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

From: Ross Walker <>
Date: Sun, 27 May 2012 18:31:09 -0700

> > 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

Chamber has never supported NBFix - At the time we were making chamber I was
told this was always a post PSF modification done in the charmm input file
ad so would need extra command line processing within Chamber to be able to
implement it. It was also a feature on the list to be added to chamber but
then unfortunately the funding was rather rudely and unprofessionally yanked
before it could get done and so it has been on the todo list ever since.

I think for now we just need someone to add a check when the parameters are
read from the prmtop file to see if any of the off diagonal elements don't
match and if so then quit in the case of cuda with an error saying it isn't
supported and we'll get to it at some point.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Sun May 27 2012 - 19:00:03 PDT
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