Re: [AMBER] nmropt modes for GPU accelerated pmemd 11

From: Andre Serobian <>
Date: Thu, 31 Mar 2011 06:43:10 +1100

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?

Kind regards,


----- Original Message -----
From: "Ross Walker" <>
To: "'AMBER Mailing List'" <>
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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Wed Mar 30 2011 - 13:00:05 PDT
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