a couple quick things to check:
1) when you built the system in leap, did you load the OPC libraries AFTER
the ff19SB library?
2) there was a patch in some of the code that is used with CMAPS, is your
AMber20 up to date with patches?
On Wed, Mar 10, 2021 at 2:27 PM Tucker Burgin <tburgin.uw.edu> wrote:
> Hi Amber users,
>
> I'm trying to develop a workflow for high-throughput simulations of
> proteins. I've got an enzyme-substrate complex parameterized with ff19SB in
> a box of OPC waters, to which I've applied hydrogen mass repartitioning
> using ParmEd with the default settings. I minimized, heated from 100 to 300
> K, and equilibrated for 1 ns using pmemd.MPI, and all that is very
> well-behaved.
>
> Now I'm trying to run longer simulations with the equilibrated structure
> using pmemd.cuda, but whenever I try to run a simulation with a timestep
> longer than 2 fs, it runs for a while (anywhere from a few hundred ps to
> several ns) before crashing with a generic error message:
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered
>
> This happens very consistently. I do *not *have this problem if I reduce
> the timestep to 2 fs, but I don't understand why. I have confirmed that the
> hydrogen mass repartitioning is correctly reflected in the topology file,
> and SHAKE is turned on. I have tried manually restarting the crashed
> simulation many times thinking that it maybe just needed more
> equilibration, but after several restarts I'm seeing no improvement. Here's
> my input file:
>
> &cntrl
>
> imin=0,
>
> ioutfm=1,
>
> ntx=1,
>
> ntxo=1,
>
> nstlim=2500000,
>
> dt=0.004,
>
> ntf=2,
>
> ntc=2,
>
> tempi=300.0,
>
> temp0=300.0,
>
> ntpr=25000,
>
> ntwx=25000,
>
> cut=8.0,
>
> ntb=2,
>
> ntp=1,
>
> ntt=2,
>
> vrand=10000,
>
> ig=-1,
>
> taup=2,
>
> &end
>
> As a further test, I have tried removing the substrate from the model
> altogether, leaving only a protein consisting entirely of standard
> residues, a single sodium ion, and the OPC water molecules, and still the
> problem persists.
>
> The output files look fine, with reasonable values for the temperature, all
> the energy terms, and the density. The only indication I have of anything
> weird in the output files is that the temperature at the 0th step is always
> about 436 K (even though tempi is 300 K and the system has been
> equilibrated at that temperature), but it returns to about 300 K by the
> next write to the output file. Here's an example output line from step 0:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 436.04 PRESS =
> -19.0
>
> Etot = -151011.7523 EKtot = 47799.7254 EPtot =
> -198811.4778
>
> BOND = 1683.1249 ANGLE = 4073.2499 DIHED =
> 2465.2522
>
> UB = 0.0000 IMP = 0.0000 CMAP =
> 381.8329
>
> 1-4 NB = 1689.6414 1-4 EEL = 19887.1333 VDWAALS =
> 21224.1537
>
> EELEC = -250215.8661 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> EKCMT = 13861.9920 VIRIAL = 14078.6721 VOLUME =
> 527955.5220
>
> Density =
> 1.0336
>
> There's nothing obviously weird to my eye going on in the simulation
> trajectory. I'm using Amber 20. Since I can't find anything wrong with the
> simulations I'm considering just writing a script to automatically restart
> my simulations whenever they crash, but I'd feel a lot more comfortable if
> I knew for sure what the problem was. Anyone have any ideas or suggestions?
> Please let me know if there's any more information I can provide.
>
> Thanks!
> -Tucker Burgin
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Received on Wed Mar 10 2021 - 13:00:02 PST
