[gmx-users] gromacs 4.6 GB/SA problem and poor performance
Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance
On 2013-01-21 09:55, Changwon Yang wrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day Can you please file a redmine issue with sample input files? http://redmine.gromacs.org Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance
On Mon, Jan 21, 2013 at 3:55 AM, Changwon Yang sht_yc...@hotmail.comwrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day Please provide the output of mdrun -version. Also ICC 11.0 is quite old. Please test whether the same issue is present with a more recent ICC or GCC compiler. Roland -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists