Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces

From: Állan Ferrari <ajrferrari.gmail.com>
Date: Tue, 1 Mar 2022 07:08:08 -0600

Thank you, Carlos.

The issue was a bad modelled loop as you guessed.



On Mon, Feb 28, 2022 at 9:34 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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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> >
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-- 
*Állan*
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Received on Tue Mar 01 2022 - 05:30:03 PST
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