Re: [AMBER] MMPBSA per residue decomposition - Calculation speed

From: Jatin Kashyap <>
Date: Wed, 31 Mar 2021 00:51:53 -0400

Hi David,

I never did the solution number 3.
Is there any tutorial that I can follow to learn “farm the snapshot” technique.

Thank you for the informative reply.

Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783

> On Mar 19, 2021, at 9:59 AM, David A Case <> wrote:
> On Fri, Mar 19, 2021, Jatin Kashyap wrote:
>> I am trying to perform MMPBSA per residue decomposition analysis using the
>> first-script located in this tutorial[1].
>> I have noticed that the calculations are taking much longer than the actual
>> MD simulation performed on GPU.
>> 1) Can I use GPU for these calculations to speed them up?
> I don't think decomoposition analysis is available on the GPU.
>> 2) how can I find out the minimum number of frames to speed
>> up the calculations without losing the accuracy?
> Start with a smaller number of frames, and keep adding more until the
> results seem to converge.
>> 3) In case GPU is not possible: Currently I am using a random number of CPU
>> cores i.e., 8, to perform this analysis. Shall I conduct the scaling study
>> and see how many cores give me the best speed.
> I would stick with one core, and use parallelization to farm the snapshots
> out to a number of separate jobs, all running at the same time.
> ...good luck...dac
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Received on Tue Mar 30 2021 - 22:00:02 PDT
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