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

From: David A Case <>
Date: Fri, 19 Mar 2021 09:59:51 -0400

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 Fri Mar 19 2021 - 07:30:02 PDT
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