Hello,
I am writing to ask for your help with optimization of 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.
However, I have no access to GPUs at this moment.
So, I am trying to continue my simulations (50 ns) using Amber22 with
pmemd.MPI, using CPUs available in HPC.
I have already 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 (>1000
hours).
Below is the last configuration I have tried to use:
#!/bin/bash
#SBATCH --partition=SP2
#SBATCH --ntasks=2 # number of tasks / mpi processes
#SBATCH --cpus-per-task=16 # Number OpenMP Threads per process
#SBATCH -J equil
#SBATCH --time=192:00:00
If anyone has any tips to help me reduce the calculation time of the
simulations, I would be very grateful.
Thank you in advance!
Kind regards,
Lucas
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Received on Thu Jul 24 2025 - 09:00:03 PDT
