On Fri, Jan 10, 2020, zizhang sheng wrote:
>
>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.
Check how shake is set in minimization vs. MD.
>
>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.
You probably need to either minimize better (you still have a large RMS
gradient at the end of minimization); or (more likely to work) heat much
more slowly: set temp0 to 100., dt=0.001, gamma_ln=10. and run a few
thousand steps of MD. I bet you'll see your potential energy go down a
lot, and (one hopes) stabilize around a new value. After that, you can
probably heat more normally.
Basically, if you still trying to do all your heating in a single run
with 2.5 million steps, that is the wrong approach. You may need to
carry out shorter MD runs with greater temperature control until the
system gets stabilized. Play with MD parameters for runs with 2.5
thousand (not 2.5 million) steps (or maybe even just 250 steps). Every
system is different, and you will need to experiment. I also notice
that you have no restraints defined -- you should consider adding
restaints to keep the solute fixed near its starting configuration until
you have done lot of MD equilibration, then slowly relaxing those
constraints. Otherwise, bad forces at the beginning may distort your
structure and it might never find its way back.
....dac
>mG
>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 - 13:00:02 PST
