[gmx-users] Performance loss during pulling simulation

[Mark Abraham]

Hi,

That sounds strange. The diagnostic information is all in the .log files,
so a side-by-side diff is often instructive. If you can't find anything
that points to a problem, please upload some log files to a file-sharing
service and share some links to think (list can't take attachments).

Mark

On Mon, Jun 27, 2016 at 12:23 PM Jan Meyer <j.meyer at uni-wuppertal.de> wrote:

>
> Dear gromacs user,
>
> i am running a system consisting of two silica-clusters (~3000 Atoms)
> who are surrounded by 85 polymer
> chains. Each polymer chain contains 200 monomer-units. The overall
> number of atoms is roughly 10^5. During the simulation i fix one of
> the clusters. The other one is
> pulled towards the fixed one. When i run this pulling simulation for
> T=300 K i get  a performance of ~6.5 ns/day. Increasing
> the temperature to 400 K leads to a performance of ~3.0 ns/day. This
> effect seems to be systematic for all the simulations i am doing on
> these and similar systems.
>
> I wonder where this performance loss comes from. So far i think it has
> to do with the pulling because i dont see this difference in
> performance doing equilibrium simulations.
>
> I would be greateful for any  explanations or suggestions to fix this.
>
> Best regards,
> Jan
>
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