Hello,
If I may: put ntf=1.
IMHO the problem is that you don't compute the harmonic spring on the bonds
involving hydrogen. In a perfect world, no problem. But because here the dt
is a little bit high you can end up with situations where shake has some
problem to recover the correct geometries, and then things can quickly go
bad.
It happen to me several times and ntf=1 is really a must for me. That won't
affect the speed of your simulations.
Also, if your system is not very much "equilibrated: at the beginning,
vrand=10000 is may be also too much. The default vrand=1000 should be
sufficient to reset the temperature at the beginning of the simulations and
stay at 300K.
Hope it helps,
Gerald.
On Thu, Mar 11, 2021 at 4:26 AM 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 Thu Mar 11 2021 - 04:00:02 PST
