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.w...@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.abra...@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.w...@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 > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
