Thankyou Jason,
Yes, I realise that now, I was hoping that there might be an alternative to
nmropt modes that will still enable us to use the nmr distance restraints in
a different way with cuda. I will try to use pmemd.mpi and see.
Kind regards,
Andre
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Thursday, March 31, 2011 6:59 AM
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 |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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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 Wed Mar 30 2011 - 13:30:02 PDT
