Hello,
Sorry for sending a message on this topic again, but I am still in trouble
with the calculation time of my MD simulations.
My system is already equilibrated and some time ago I successfully ran
production
simulations starting from it, using GPU resources.
As I have no access to GPUs at this moment, I am trying to continue my
simulations (50 ns) with pmemd.MPI, using CPUs.
As it is a continuation of previous simulations, I cannot do significant
modifications in my simulation setup that might result in improved
performance.
Therefore, I have tried to configure my script in several ways, aiming
to optimize
the use of the available nodes/CPUs to accelerate the calculation,
but the estimated time to complete the simulations remains very high.
Below is the last configuration I have tried to use:
#!/bin/bash
#SBATCH --partition=SP2
#SBATCH --ntasks=32
#SBATCH --cpus-per-task=1
#SBATCH -J prod
#SBATCH --time=192:00:00
I would appreciate it if you have any tips to reduce the calculation time
of the simulations.
Thank you in advance!
Kind regards,
Lucas
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Received on Thu Jul 31 2025 - 14:30:02 PDT
