for ff19SB problems, make sure your Amber version is completely updated
with current patches. There was a fix a while back that corrected an error
that could lead to failures with some force fields including ff19SB.
Information on applying patches is found here:
http://ambermd.org/AmberPatches.php
for the problem with ff14SB, I did not see the original post. More details
would be helpful, especially about the system you are simulating (is it
only protein, or more? did you use any other parameters except ff14SB?
Where were the initial coordinates obtained?).
On Mon, Jul 19, 2021 at 9:46 AM Gerardo Zerbetto De Palma <
g.zerbetto.gmail.com> wrote:
> Hi we are using ff14SB forcefield and the errors still appear.
> Thanks for the help!
> Regards
>
> Gerardo Zerbetto
>
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> El vie, 16 jul 2021 a las 18:29, Rafał Madaj (<rmadaj.cbmm.lodz.pl>)
> escribió:
>
> > Hi,
> >
> > Which force field are you using? I had exactly same problem with ff19SB.
> > After changing into ff14SB the problem disappeared.
> >
> > Regards,
> >
> > Rafal
> >
> > On 16.07.2021 18:01, Gerardo Zerbetto De Palma wrote:
> > > Hi everyone.
> > > We were trying to run some simulations of a membrane protein on an
> NVIDIA
> > > TITAN V and got stuck by some cudaMemcpy that came in different
> flavors:
> > >
> > > cudaMemcpy GpuBuffer::Upload failed unspecified launch failure
> > > cudaMemcpy GpuBuffer::Download failed unspecified launch failure
> > > cudaMemcpy GpuBuffer::Download failed an illegal instruction was
> > encountered
> > >
> > > Firstly we started running the sim using amber 18, restarting the sim
> > every
> > > 5 nanoseconds to get consecutive 5ns trajectories. After simulating 25
> > > nanoseconds, the program stopped randomly. Then we tried to repeat the
> > > simulation that had failed (using the same random seed and initial
> > > coordinates) and the simulation succeeded, but the same error came up
> in
> > a
> > > subsequent simulation. These errors kept coming at a random timestep
> when
> > > we restarted the simulations. Energies in the output seemed to be OK
> and
> > > simulations sometimes proceeded without errors when restarted. Hoping
> > that
> > > this was a bug, we compiled amber 20 and ran the same simulations and
> had
> > > the same random cudaMemcpy errors. Just to check if the simulated
> system
> > > was fine, we are also running it in a RTX2080 with amber 18 without
> > > problems, so far.
> > >
> > > We are running out of ideas here so here we are reaching out to the
> > > community for some help in this matter. We will appreciate every idea
> or
> > > question that can enlighten us to solve this puzzle.
> > >
> > > Regards!
> > > Gerardo Zerbetto De Palma
> > >
> > > <
> >
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Received on Mon Jul 19 2021 - 07:30:02 PDT
