[gmx-users] increasing md run speed

[Mark Abraham]

Hi,

You might be, but you need to look at the bottom of the log files for
performance feedback. What is common and different?

Mark

On Sun, Jun 24, 2018 at 6:23 AM neelam wafa <neelam.wafa at gmail.com> wrote:

> 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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