Re: [AMBER] Size limit for amber

From: Ibrahim M. Moustafa <>
Date: Mon, 10 Dec 2018 13:44:41 -0500

Thank you for the reply. I'm planning to use the pmemd.cuda for the gpu. I just
wanted to do the minimization using sander.MPI
  For editing the suggested file, do I need to re-compile the whole package?

On Mon, Dec 10, 2018 01:34 PM,, AMBER Mailing List
<> wrote:
On Mon, Dec 10, 2018, Ibrahim M. Moustafa wrote:
>> I'm trying to do MD simulations using AMBER18 for large systems in
>>solvent. Amber seems able to be able to handle a size of 1.09 million atoms
>>very well.However, trying to minimize a system with over 2 million atoms did
>>not work, giving the error message given below. The minimization tried using
>>sander.MPI with -np 32. The computer running the simulations has 128 GB RAM
>>4x 1080Ti GPU.
>First, use pmemd.MPI on a cpu. It is *much* better suited to large
>simulations than in sander.MPI. You can also try pmemd.cuda, which
>should be much faster if you have enough memory. (With modern cards
>like the 1080Ti, don't try pmemd.cuda.MPI unless you have time on your
>hands, and are prepared for poor scaling across multiple GPUs.)
>(If you really need sander, editing MAXPR as suggested in the error
>messages stands a good chance of fixing the problem.)
>I've simulated systems with up to 3.5 million atoms with pmemd. Not
>sure what the actual limit is, and it probably depends on hardware.
>...good luck...dac
>AMBER mailing list

Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park, PA16802

Tel (814)863 5940
Fax (814)865 7927

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Received on Mon Dec 10 2018 - 11:00:05 PST
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