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

From: Jason Swails <>
Date: Mon, 28 May 2012 09:40:27 +1000

On May 27, 2012, at 11:28 PM, case <> wrote:

> On Sun, May 27, 2012, Jason Swails wrote:
>> Some words of warning: pmemd.cuda will ignore any off-diagonal
>> A/B coefficient changes. It recalculates sigma and epsilon and
>> recombines those when it calculates the Lennard Jones term for each
>> atom pair. Therefore, the only commands that will actually work for
>> pmemd.cuda are addLJType and changeLJSingleType (the changePair commands
>> will not work on GPUs).
> Ouch...let's make this a priority to get fixed. Does pmemd.cuda give the
> wrong answers without any warnings?

No error messages/warnings. It implicitly assumes nobody (or parmed) has messed with off-diagonal (or only-diagonal) elements of the coefficient matrices). The only way to warn really would be to check that all of the computed coefficients match with the ones in the prmtop. I can work on this check when I get a chance (but being in a state of flux right now I don't know when that will be).

I discussed this to a decent extent with Scott, who will likely chime in here. The issue is that the performance hit will be pretty severe if we can't fit the A and B coefficient matrices in shared memory. Since the shared memory is pretty much tapped out at this point, it's likely that it won't fit and performance will severely suffer. That's why the decision was made to actually apply the combining rules each time rather than use pre-computed ones.

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.

I hope this clarifies things a bit.

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 - 17:00:01 PDT
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