Hi Nihal,
> I am going to make free energy simulations of a protein via implicit
> solvent
> (igb=5) on GPU. My question is whether gbsa still not applicable on
> pmemd.cuda. Is there a way to implement gbsa consideration while runing
> on
> GPUs? I have seen that a group from Stanford U. has managed to use such
> a
> combination (although on a different platform called folding.home, they
> should have developed a "patch" themselves). Seeing that I wanted to
> check
> if there is any chance of applying gbsa+GPU combination.
Unless someone wants to volunteer to write it there is currently no support
for GBSA on GPUs. Right now we are focused on what I consider more important
priorities given the GBSA approximation is pretty questionable at best.
Scott Le Grand can chime in with his opinions on the subject here.
I would suggest that your best approach is to run GB with pmemd.cuda with
gbsa=0. Then when you come to do the MM-PBSA/GBSA calculations just run the
single point energy calculations in sander with GBSA turned on - since it is
only single point energies it will be very quick. If you have evidence that
running the actual MD with GBSA turned on rather than just straight GB
ultimately gives better binding energies than the MM-PBSA/GBSA post
processing approach I'd be interested to read it.
The other option is to go into the PMEMD code, remove the check for GBSA=0
with cuda and then place GPU to CPU upload and download calls as appropriate
around the CPU GBSA calculation code. This will suffer on performance though
because of the continuous GPU/CPU synchronization going on.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Oct 04 2011 - 12:00:05 PDT
