Re: [AMBER] error in MD simulation

From: Jason Swails <>
Date: Thu, 25 Jun 2015 10:47:59 -0400

On Thu, Jun 25, 2015 at 10:17 AM, <> wrote:

> Dear Amber users,
> I'm trying to perform a simulation of a dimeric protein (about 90 aa for
> each chain) solvated using TIP3P water model in a cubic box, total number
> of atoms = 66656. I run the simulations with PMEMD on NVIDIA GPU. After the
> minimization, the calculation crashes with the following error:
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered
> At line 137 of file inpcrd_dat.F90 (unit = 9, file = 'heat_solv.rst')
> Fortran runtime error: End of file

​This looks like the coordinate file was truncated. What are the contents
of heat_solv.rst? It also seems strange to me to see *both* of the error
messages you printed above in the same simulation. Maybe you saw the
cudaMemcpy error in the minimization, and then the heating stage failed
because the restart wasn't written?

What version of Amber are you using?

> I red in the blog that it could be a restraints problem but I received the
> same error even when I set ntr=0. In attachment you can find the input
> parameters that I tried to use for my simulation...this is only the early
> stage after that I plan to carried out the equilibration in NPT and the
> production in NVT ensemble.
> Could you please help me or give me any advice about this error?

​Common tips: run minimizations using the CPU code, since fixed-precision
numbers can overflow more often than double precision. Whenever you get an
error, check the CPU code to see if you get an error there as well. Error
messages are usually better when using the CPU code, so that is always a
good first step in debugging.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 25 2015 - 08:00:03 PDT
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