Hi there,
I am using Amber with the SIRAH force field on our national HPC. When I try to restart my simulation, I get an MPI error.
Would I be correct in saying that the following command is how to restart an amber simulation?
srun pmemd.cuda_SPFP.MPI -O -i md_WT4.in -p sim_cg.prmtop -c md.ncrst -o md_2.out -r md_2.ncrst -x md_2.nc
The original MD calculation command is the following:
srun pmemd.cuda_SPFP.MPI -O -i md_WT4.in -p sim_cg.prmtop -c sim_eq2.ncrst -o md.out -r md.ncrst -x md.nc
I have consulted the Amber24 pdf, and have set ntx to 5, irest to 1 and imin to 0 as advised. I am new to Amber, so I am not sure where I am going wrong.
Thank you.
Kind Regards,
Niamh
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Received on Thu Apr 09 2026 - 02:30:03 PDT
