[AMBER] MMPBSA per residue decomposition - Calculation speed

From: Jatin Kashyap <jk435.njit.edu>
Date: Fri, 19 Mar 2021 06:11:52 -0400

Dear AMBER Community,

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.
Can you please help me with the below points:

1) Can I use GPU for these calculations to speed them up?

2) If GPU is not possible, can I reduce the number of frames in the trajectory file without losing the accuracy of the results beyond a certain threshold? If yes, how can I find out the minimum number of frames to speed up the calculations without losing the accuracy?

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. If yes, how shall I check the performance statistics since .out and .err file doesn’t contain the corresponding information.

Thank you.


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
Email- jk435.njit.edu

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Received on Fri Mar 19 2021 - 03:30:02 PDT
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