Hi... you have to implement the algorithm using parallel paradigma (MPI, openmp, thread....) Alternatively, there is a workaround to bypass the serial rmsd matrix building (the most time consuming part). g_cluster reads a rmsd matrix as input, you can run different rmsd instance in parallel, using appropriate input, in order to obtain the different rows of the matrix. Next, you have to collect these outputs through in order to have the .xpm file through an appropriate script (that you have to write). This matrix can be used as input to g_cluster that will use it to calculate clusters
Francesco 2012/10/2 R.Vidya Rajendran (10PHD013) <vidya2...@vit.ac.in> > Dear Friends, > > Gromacs script such as g_cluster takes lot of time to complete in a > single machine. Is their any way to give this job to a cluster machine > like mdrun. Since mdrun is MPI enabled so I can easily execute it on > cluster. > > Anybody in group have any clue that how we can execute g_cluster > command on a cluster machine ? > > > regards > Vidya > -- > gmx-users mailing list gmx-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 > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list gmx-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
