I was looking into doing FEP calculations rather than using MM-PBSA/GBSA.
I will try changing the pmemd code, as you said it will slow things down but
might be worth a shot.
Thanks,
Nihal
On Tue, Oct 4, 2011 at 1:43 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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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--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Tue Oct 04 2011 - 12:30:05 PDT
