From: raghav singh (raghavbioinfo_at_gmail.com)
Date: Mon Jan 25 2021 - 06:02:52 CST
Dear NAMD Developers and Users,
I have a protein(solvated and neutralized with 0.15mM NaCl concentration)
simulation system under classical MD scenario with charmm36 ff parameters
implemented in VMD/NAMD.
I have prepared my system with both GROMACS and NAMD* (*preferred because I
would like to run Accelerated MD later on). The system consists of 148943
atoms all together, I have tried to test the speed and scaling of NAMD
using 1,2,4,8,16 and 32 nodes and found a linear scaling. I get ~50ns/day
of yield with NAMD on 32 nodes (768 processing cores), while if I run the
similar system with gromacs on 20 nodes (480 processing cores) and I get
~270ns/day.
Would it be possible for someone in the group to look at my issue, as
~150000 atoms simulation system should not require this much of resources
to run this short simulation. I think I am wasting my HPC resources and I
am in need of dire intervention from experts.
Please find Attached the configuration and run script. I would greatly
appreciate your expert intervention and help, so that I can make the
best use of the HPC resources.
Thanking you
Best regards
Raghav
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