I will try to narrow down the problem and make a proper report including test cases (cause I have several)...
I find very important to fix this issue because the GPU code is orders of magnitude faster than the CPU one and using the CPU for huge systems is sometimes "impractical"...
From my observations, it seems the GPU code may be neglecting some VDW interactions contributing to the energy during the minimization. As a result almost no change is done to the coordinates/energy, or even worst I've seen cases in which the minimization procedure places atoms too close to each other (i.e. less that 1 armstrong apart!!!).
At first, I thought it was an issue related to SIRAH, but now I realize it isn't...
Best,
Matías
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 16 de Diciembre 2020 11:45:58
Asunto: Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating
Dear Chris, Ross and David,
I've seen the similar issue in some of my simulation, but at coarse-grained level using SIRAH...
So far I could track the issue to the minimization using the GPU code of AMBER 18 (I didn't test AMBER 20 yet!)...
Please try using the CPU code for minimization and the GPU for MD, As David suggests... that worked in my case.
Sorry, I've been very busy to fill a proper bug report...
All the best,
Matias
----- Mensaje original -----
De: "David A Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 16 de Diciembre 2020 11:02:54
Asunto: Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating
On Tue, Dec 15, 2020, Chris Lee wrote:
>
>I recently ran the attached job script (runMD.sh) and got the following error:
Try this:
Run the minimization and a (short) heating step on the CPU. The switch
to GPU.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 16 2020 - 07:30:02 PST
