[gmx-users] increasing md run speed

Mark Abraham mark.j.abraham at gmail.com
Sat Jun 23 09:07:23 CEST 2018


That's an energy minimisation output file. It's too short to get a
meaningful estimate of performance, and will anyway not be representative
of what the simulation will achieve. More recent versions of GROMACS won't
even report on performance for them.


On Sat, Jun 23, 2018, 04:56 neelam wafa <neelam.wafa at gmail.com> wrote:

> Dear gmx users!
> I am running md simmulation of a protein with different ligands but the
> speed is decreasing with every simmulation. In first one it was 25hrs/ns,
> for second one it became 35 hrs/ns then 36hs/ns. what can be the reason?
> I am using this command for the run.
> How to select the value of x if I use this command to increase the speed.
> Following is the detail of the cores used and the hardware i am using.
> Running on 1 node with total 2 cores, 4 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Core(TM) i3-2370M CPU @ 2.40GHz
>     SIMD instructions most likely to fit this hardware: AVX_256
>     SIMD instructions selected at GROMACS compile time: AVX_256
> Reading file em.tpr, VERSION 5.1.5 (single precision)
> Using 1 MPI thread
> Using 4 OpenMP threads
> Looking forward for your help and cooperation.
> Regards
> --
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