On Thu, Jan 09, 2020, zizhang sheng wrote:
>
>When I run MD for glycoproteins in Amber18 pmemed.cuda.MPI, it always
>crash with the memory error when heating from 0k to 300k.
>
>&cntrl
>nstlim=2500000, dt=0.002, ntx=1, irest=0, ntpr=20000, ntwr=20000, ntwx=20000,
Try reducing nstlim by four orders of magnitude (i.e. to 250) and set
ntpr=1. Do you see a failure right at the beginning? Do the energies
at step 0 (assuming they are printed) match the energies at the end of
the minimization step? If you get several steps, look for any
instabilities, such as the temperature rising very quickly, etc.
Start with just using pmemd itself; then you can see if there is a
difference in using pmemd.cuda. Use of pmemd.cuda.MPI is only for
experienced users, and definitely should not be used when problems arise
and debugging is needed.
>tempi =0.0, temp0=300.0, ntt=3, gamma_ln=1.0,taup=5,
>vlimit=20,
>ntb=1, ntp=0,
>cut=12,
Stick to the default value of 8.
...good luck...dac
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Received on Thu Jan 09 2020 - 10:30:01 PST
