Hi All,
When I run MD for glycoproteins in Amber18 pmemed.cuda.MPI, it always crash with the memory error when heating from 0k to 300k. The simulations without glycans but with identical MD parameters are all good. The glycan I added is MAN3 from Glycam. Tleap did not show any error. I also tried with the vlimit=20 option suggested in previous threads but run into the same error. I also tried with pmem.cuda and pmem.MPI, they all give the same error. The GPU card is 1080Ti. I wonder if anyone has the similar issue when simulating glycoprotein.
The steps I am running are:
1) minimize the solution
2) minimize the whole system
3) heating
4) equilibration
Attached is the parameters for heating.
Thanks,
Zizhang Sheng
&cntrl
nstlim=2500000, dt=0.002, ntx=1, irest=0, ntpr=20000, ntwr=20000, ntwx=20000,
tempi =0.0, temp0=300.0, ntt=3, gamma_ln=1.0,taup=5,
vlimit=20,
ntb=1, ntp=0,
cut=12,
ntc=2, ntf=2,
nmropt=1,
iwrap=1,
nrespa=1,!frequency of steps to evaluate slowly-varying terms
/
&wt type='TEMP0', istep1=0, istep2=900000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=900001, istep2=2500000, value1=300.0, value2=300.0 /
&wt type='END’ /
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Received on Thu Jan 09 2020 - 06:30:02 PST
