[gmx-users] increasing md run speed

[neelam wafa]

Hi, I have run a 100 ps simmulation  of the same protein with different
ligand and its producing 0.445ns/day and 53.988 hr/ns.
while this was 25hr/ns for the first simmulation of the same protein. Am I
doing something wrong?
I have been using the same md.mdp file for all the simmulations.

Regards

On Sat, Jun 23, 2018 at 7:07 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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