Dear Amber users:
I'm now using Amber 20 and RTX 2080Ti to simulate a membrane protein system. This system contains ~80,000 atoms in total. In regular simulations, the speed is about 110 ns/d, which is quite acceptable. However, once I turned on the Thermodynamic Integration module, the speed drops sharply to only 24 ns/d. This is quite strange, since the manual says "Performance of the PME TI pmemd implementation is approximately 75% that of a regular PME MD simulation", and this also makes sufficient sampling difficult.
Does anyone have a clue to this? Any help is appreciated.
bests,
Kevin
mdin parameters:
imin=0, irest=1,ntx=5, ntt=3, gamma_ln=1.0, temp0=310.0, cut=9.0, nstlim=2500000, dt=0.002, ntc=2, ntpr=500, ntwx=50000, ntwr=50000, ntxo=2, ioutfm=1, iwrap=1, nmropt=1,
icfe=1, clambda=0.015920, timask1=":913.Na+", timask2="", ifsc=1, scmask1=":913.Na+", scmask2="", scalpha=0.05, scbeta=12,
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Received on Wed May 10 2023 - 20:30:02 PDT
