Re: [AMBER] Problem with heating the system

From: Pratul Agarwal <>
Date: Wed, 24 Apr 2019 12:14:12 +0000

Do you mean it is about 300,000 atoms? GTX Titan has enough memory to run such systems. Is there another simulation using the same GPU?

Is your system well equilibriated? Can you change ntpr=1 (or add ntwe=1) and see if the simulations runs for a few steps before it crashes? Check md.out and mdinfo files for clues.

Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 4/24/2019 7:53 AM, ATUL KUMAR wrote:

Thank you for reply David my system size is roughly 3 lack atoms. And I
tried to run the heating script on CPU and it was running fine. The Ram
dedicated to CPU in my machine is 32GB.

On Wed, 24 Apr 2019, 5:17 pm David A Case, <><> wrote:

On Wed, Apr 24, 2019, ATUL KUMAR wrote:

Keep DNA fixed with weak restraints

Aside: these are actually very strong restraints, not weak ones.

cudaMalloc GpuBuffer::Allocate failed out of memory

Run your job on the CPU version of pmemd: the CPU version generally
gives more helpful error messages. You don't say how big your system
is: it could really just be that you don't have enough memory. Hard to
say without knowin more.


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Received on Wed Apr 24 2019 - 05:30:02 PDT
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