GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
Hi, I’m currently working on my Molecular Dynamics (MD) Simulation project using Gromacs in Windows Subsystem for Linux (WSL) Environment. My hardware is Intel(R) Pentium(R) CPU 5405U @ 2.30GHz RAM 4GB with x64-based processor type of system. I’ve completed 10ns mdrun using CHARMM36 FF just fine, but I’m concerned because my result only came out after 9 days and the gromacs performance was pretty low, 1.517 ns/day. I’ve tried uninstalling and updating my gromacs but the performance didn’t improve that much (before gromacs update it was around 0.66 ns/day). I’m wondering if this happened because my hardware is not compatible enough for Gromacs or maybe there’s something i missed? i really appreciate it if there’s someone who can tell me what I can possibly do to solve this. Thanks in advance.
Hi,
It’s difficult to know whether this performance is good or bad without knowing the size (number of atoms) of your system. You say that you tried updating GROMACS, but the performance did not improve that much, then you report an improvement from 0.66 to 1.52 ns/day. That’s a factor 2.3 improvement. That’s quite significant.
Hi, thanks for the reply. Actually there are 56158 atoms on my system, and I’ve seen some people on this platform working with gromacs using similar size system as me, but their gromacs performance was far way better (I’ve seen some with 21 ns/day performance etc) so I was wondering if there’s something wrong with mine. There’s indeed a significant improvement after the update, but I think it will be nice if I can find a way to improve the performance since my original intention is to run my samples on 100ns and there’s a deadline approaching.
The mobile processor you use has just 2 cores and 4 threads ( Intel® Pentium® Gold 5405U Processor). With a system containing >50k atoms, I don’t think you will get any significant performance boost.
Yeah, I’ve been thinking if that was the case. Thanks for making it clear tho! guess I just have to stick with whatever I can do right now.