Hi everyone,
I am attempting to run MD simulation of a 262,572 atoms system (protein
attached to a lipid membrane) on a phi 7120P.
It takes 38h for 2ns and I am wondering how I could accelerate things.
I use:
pmemd.mic_offload.MPI
nodes=1
ntasks-per-node=20
cpus-per-task=1
gres=mic:1
and the input file is:
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=1000000, ntt=3, gamma_ln=1.0,
temp0=310.0,
ntpr=20000, ntwr=500000, ntwx=20000,
dt=0.002, ig=-1,
ntb=2, ntp=2, cut=10.0, barostat=1, ioutfm=1, ntxo=2
Please, let me know if you need more info about my system.
Thank you in advance.
Cheers,
Sofia
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Received on Tue Mar 14 2017 - 07:30:02 PDT
