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.
[1]
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
——
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 19 2021 - 03:30:02 PDT
