Hi It is a small ligand decoupling from its native protein and there are orientational restraints near high decoupled region. I am using gcc and gfortran compilers . Jagannath
On Tue, Mar 15, 2016 at 6:54 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > No, the free energy kernels run on the CPU. This large change must mean > that you have a relatively large fraction of the system participating in > perturbed interactions. > > What compiler are you using? The free energy kernel is a bit "sensitive" > (to put it mildly) and I do remember seeing much better performance with > some compilers than others. > > -- > Szilárd > > On Tue, Mar 15, 2016 at 2:18 PM, jagannath mondal <jm3...@columbia.edu> > wrote: > > > Dear Gromacs users > > I am trying to perform Free energy peturbation calculation in presence > of > > distance, angle and dihedral-restraint for a protein-ligand system. > > However, I am finding, on turning on the FEP calculation, the performance > > of gromacs5.1.1. in a gpu-based workstation significantly gets reduced. > the > > gpu/cpu ratio reduces from 1 to 0.234 on turning on FEP module. I was > > wondering whether FEP-module is still not using gpu-based optimization. > > Jagannath > > -- > > 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.