Re: [AMBER] issues with pmemd.cuda

From: David A Case <>
Date: Thu, 25 Apr 2019 13:43:32 -0400

On Thu, Apr 25, 2019, Veenis, Andrew Jay wrote:
>I am using MD to study a RNA enzyme. When I equilibrate the system on
>CPUs at our university's cluster using pmemd.MPI, I get sound results
>where the enzyme's configuration remains close to that of the crystal
>structure it was based on. Upon using the identical input files (same
>md5sum values) to run the MD on our computer using pmemd.cuda, residue
>4 changes from a southern to a northern pucker during NPT equilibration
>(see 09_npt_eq_pucker.dat). This conformational switch does not occur
>when the simulations are run using CPUs.
>I am using a computer purchased from Exxact to run AMBER. Ross Walker
>had me run DPFP and SPFP tests and they gave no indication that there is
>anything wrong with the AMBER installation.
>The system was minimized using CPUs. I have attached the relevant files
>to this email. Am I doing something wrong or is there a bug in the GPU

Remember that MD is a very chaotic process, and you should not expect
the details of any particular trajectory to be reproducible when using a
different computer or program or compiler. (In fact, with pmemd.MPI,
you won't even get the same trajectory when re-running with the same
exectuable on the same computer--this is because the reductions among
various MPI threads are not deterministic.)

So: we(you) need to know if this pucker flip always happens on the GPU,
and never happens on the CPU, under repeated simulations. If you
haven't already done so, set barostat=2 for NPT: that can be somewhat
less perturbing that running with the default barostat=1.

It may also be worth checking your time-step (dt). It's more likely
that you will get collision-induced conformational changes if you are on
the bleeding-edge (by using 0.004 with HMassRepartition) than with
time-steps of 0.001 or 0.002. This can be especially true during

...good luck....dac

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Received on Thu Apr 25 2019 - 11:00:04 PDT
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