Hi David,
Thanks for the suggestions.
If I run PMEMD.MPI, sometimes the heating started for a few steps and die. For PMEMD.CUDA, it sometimes die at the beginning. Here is the output from minimization and start of heating:
Energy minimization:
NSTEP ENERGY RMS GMAX NAME NUMBER
5214 -1.5853E+05 4.6706E+01 8.2567E+03 HB2 1631
BOND = 6923.8637 ANGLE = 1092.5932 DIHED = 4959.0141
VDWAALS = 12825.5765 EEL = -215473.5524 HBOND = 0.0000
1-4 VDW = 11265.8123 1-4 EEL = 19879.2193 RESTRAINT = 0.0000
Heating:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -164877.0775 EKtot = 0.0000 EPtot = -164877.0775
BOND = 624.2695 ANGLE = 1092.5932 DIHED = 4959.0141
1-4 NB = 11265.8123 1-4 EEL = 19879.2193 VDWAALS = 12761.0383
EELEC = -215459.0242 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
It seems the bond energy change dramatically between the two files.
I am now running the same heating script with vlimit=10. For both PMEMD.MPI and PMEMD.CUDA, the heating step finished ok. But the output shows lots of velocity exceeding 10, even in thousands. I wonder if this will help find the cause.
Best,
Zizhang
> On Jan 9, 2020, at 9:18 AM, zizhang sheng <shengzizhang.gmail.com> wrote:
>
> 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 Fri Jan 10 2020 - 10:00:02 PST
