Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed

From: David A Case <>
Date: Mon, 24 Sep 2018 07:39:26 -0400

On Mon, Sep 24, 2018, Aravind Ravichandran wrote:

> I wanted to run my production MD with HMR. So, after preparing my
> simulation, running minimization and equilibration steps, I used parmed
> to change the H-mass.
> {
> parmed prmtop
> HMassRepartition
> outparm hmr.prmtop
> }
> After this I ran my production where I got the following error:
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered

Usual debugging strategy: run a short simulation with ntpr=1. Do you
see anything that helps? Does the above error occur before the first
energy calcualation or somewhere later on?

Second strategy: run the same short simluation with the CPU version. Is
there any difference?

You may also want to try a constant volume simulation, to see if the
instability in your system is related to pressure or density changes.

...good luck...dac

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Received on Mon Sep 24 2018 - 05:00:02 PDT
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