there can be many reasons, but most often it is due to high
energies/forces. You might want to check the energies and gmax at the end
of the minimization. Also, check any non-standard parameters that you used.
If you're simulating 1GNX, it looks like the PDB is missing some regions.
How were they modeled?
minimization prior to MD doesn't usually need to be so long - I find that
500 steps or so is usually enough.
Using a smaller ntpr might help you see what happens prior to the error (in
case it goes past step 0).
On Sun, Feb 27, 2022 at 8:18 PM Állan Ferrari <ajrferrari.gmail.com> wrote:
> Hi,
>
> I am running some simulations for homologous proteins.
> As part of my protocol, I run:
> - Minimization: 10,000 steps
> - NVT equilibration: 10,000 steps and restraints in all protein atoms
> - NPT equilibration: 10,000 steps and restraints in all protein atoms
> (k=10)
> - NPT equilibration: 10,000 steps and restraints in all backbone protein
> atoms (k=10)
> - NPT equilibration: 10,000 steps and w/o restraints
> - Production run at 300 K
>
> I'm getting an error right after minimization, in the NVT step.
>
> Error: an illegal memory access was encountered launching kernel
> kClearForces
>
> The NVT equilibration starts but does not proceed. See the nvt.log file
> attached.
>
> Is this a common error? What can I do to solve this?
>
> Regards,
>
>
> --
> *Állan*
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Received on Mon Feb 28 2022 - 08:00:03 PST
