Dear Mu,
I would highly recommend upgrading to AMBER 12 - especially if you want to
run implicit solvent on GPUs. GB in AMBER 11 uses a LOT of memory. In
AMBER 12 with the latest updates it uses so little memory that you can
easily run multiple million atom GB runs in a few GB.
I'd also note that it is difficult to buy GTX580s these days. You ideally
want to get a GTX680 (much better performance) which is likely cheaper
than a 580 these days. Or alternatively a GTX-Titan which completely
screams (and has 6GB of memory).
Both the 680 and titan require AMBER 12 though.
The following paper has the GB atom limit numbers for Amber 11:
http://www.wmd-lab.org/papers/2012_JCTC_GPU_GB_Paper_ct200909j.pdf
While
http://ambermd.org/gpus/ has them for Amber 12.
Short answer.
1.5GB limit is about 20,000 atoms for GB in AMBER 11
1.5GB limit is about 650,000 atoms for GB in AMBER 12
All the best
Ross
On 3/21/13 8:24 PM, "Mu Xia" <muxiachuixue.163.com> wrote:
>Hi all,
>
>
>I am planning to buy a GPU card for acceleration of AMBER11. After a
>round of search, GTX580 was focused.
>
>
>The scale of MD is usually 30,000-50,000 atoms size. So, here come two
>questions:
>
>
>1. Which memory should the GPU card be in my case? 1.5 G or 3 G? Is 1.5 G
>enough or not?
>
>
>2. How many "ns" could the MD run in one day with GTX 580 1.5 G version?
>
>
>Thanks!
>
>
>Mu Xia,
>Zhejiang University
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Received on Fri Mar 22 2013 - 11:30:03 PDT
