Dear Jason,
Just wanted to check if there was an ETA on enabling nmropt modes for pmemd.cuda? This would immensely help with current experiments, and as you can tell we are very eager to use this function.
Kind regards,
Andre
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, 31 March 2011 6:59 AM
To: AMBER Mailing List
Subject: Re: [AMBER] nmropt modes for GPU accelerated pmemd 11
On Wed, Mar 30, 2011 at 12:43 PM, Andre Serobian < serobian.a.student.unsw.edu.au> wrote:
> Dear Prof. Walker,
>
> Thankyou for your reply. We trying to use nmr distant restraints from
> experimental results and processing speed is important to us so we
> were hoping to utilise our GPU's for this. However, as nmropt=1 we are
> unable to use pmemd.cuda and so sander.mpi is the only way we can
> include the nmr 7-col distance restraint file for the md.
>
> Are there any other methods to increase processing speed other than
> increasing the number of cpu's with sander.mpi?
>
You can use pmemd (or pmemd.MPI) to my knowledge, just not pmemd.cuda.
pmemd is still considerably faster than sander for the capabilities that it DOES possess.
Good luck,
Jason
>
> Kind regards,
>
> Andre
>
>
> ----- Original Message -----
> From: "Ross Walker" <ross.rosswalker.co.uk>
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Sent: Thursday, March 31, 2011 5:27 AM
> Subject: Re: [AMBER] nmropt modes for GPU accelerated pmemd 11
>
>
> Hi Andre,
>
> > Is the any news on when nmropt modes will be enabled for GPU
> > accelerated version of pmemd 11?
>
> It is my hope to have this added as a feature for PMEMD 12, depending
> on NSF funding etc. It is getting a little too much now to keep
> putting out long patches for AMBER 11.
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Nov 10 2011 - 02:00:02 PST
