Oh that makes sense! Elsaid, issue:
module load gromacs/5.0.4 "module load gromacs" defaults to an ancient release of gromacs. Sam > On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/9/15 1:08 PM, Samuel Flores wrote: >> Hi Justin, >> >> Is gmx the same as ngmx? Here are the binaries in the Uppmax gromacs >> directory: >> > > gmx refers to the single binary provided as of 5.0, which is the new setup. > What appears here is a (very) outdated version of GROMACS, and usage needs to > be adjusted accordingly. > > -Justin > >> [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/ >> GMXRC g_anadock_d g_cluster g_densorder_d g_enemat >> g_helixorient_d g_morph g_pme_error_d g_rmsdist g_select_d >> g_traj genbox make_edi_d trjcat_d >> GMXRC.bash g_anaeig g_cluster_d g_dielectric g_enemat_d >> g_hydorder g_morph_d g_polystat g_rmsdist_d g_sgangle >> g_traj_d genbox_d make_ndx trjconv >> GMXRC.csh g_anaeig_d g_clustsize g_dielectric_d g_energy >> g_hydorder_d g_msd g_polystat_d g_rmsf g_sgangle_d >> g_tune_pme genconf make_ndx_d trjconv_d >> GMXRC.zsh g_analyze g_clustsize_d g_dipoles g_energy_d >> g_kinetics g_msd_d g_potential g_rmsf_d g_sham >> g_tune_pme_d genconf_d mdrun trjorder >> completion.bash g_analyze_d g_confrms g_dipoles_d g_filter >> g_kinetics_d g_nmeig g_potential_d g_rotacf g_sham_d >> g_vanhove genion mdrun_d trjorder_d >> completion.csh g_angle g_confrms_d g_disre g_filter_d >> g_lie g_nmeig_d g_principal g_rotacf_d g_sigeps >> g_vanhove_d genion_d mdrun_mpi xplor2gmx.pl >> completion.zsh g_angle_d g_covar g_disre_d g_gyrate >> g_lie_d g_nmens g_principal_d g_rotmat g_sigeps_d >> g_velacc genrestr mdrun_mpi_d xplor2gmx.pl~ >> demux.pl g_bar g_covar_d g_dist g_gyrate_d >> g_luck g_nmens_d g_protonate g_rotmat_d g_sorient >> g_velacc_d genrestr_d mk_angndx xpm2ps >> do_dssp g_bar_d g_current g_dist_d g_h2order >> g_luck_d g_nmtraj g_protonate_d g_saltbr g_sorient_d >> g_wham gmxcheck mk_angndx_d xpm2ps_d >> do_dssp_d g_bond g_current_d g_dos g_h2order_d >> g_mdmat g_nmtraj_d g_rama g_saltbr_d g_spatial >> g_wham_d gmxcheck_d ngmx >> editconf g_bond_d g_density g_dos_d g_hbond >> g_mdmat_d g_options g_rama_d g_sans g_spatial_d >> g_wheel gmxdump pdb2gmx >> editconf_d g_bundle g_density_d g_dyecoupl g_hbond_d >> g_membed g_options_d g_rdf g_sans_d g_spol >> g_wheel_d gmxdump_d pdb2gmx_d >> eneconv g_bundle_d g_densmap g_dyecoupl_d g_helix >> g_membed_d g_order g_rdf_d g_sas g_spol_d >> g_x2top grompp tpbconv >> eneconv_d g_chi g_densmap_d g_dyndom g_helix_d >> g_mindist g_order_d g_rms g_sas_d g_tcaf >> g_x2top_d grompp_d tpbconv_d >> g_anadock g_chi_d g_densorder g_dyndom_d g_helixorient >> g_mindist_d g_pme_error g_rms_d g_select g_tcaf_d >> g_xrama make_edi trjcat >> >> >> Elsaid, >> >> Regarding Justin’s suggestion, on Uppmax I believe the full path would be: >> >> source /sw/apps/gromacs/4.6.3/tintin/bin/GMXRC.bash >> >> >> However I think you already issued >> >> module load gromacs >> >> which might source GMXRC . >> >> Sam >> >> >>> On Nov 9, 2015, at 17:56, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 11/9/15 11:55 AM, Elsaid Younes wrote: >>>> Hi, >>>> >>>> Thank you for your response. >>>> When writing gmx, it gives the command not found. (Note I use windows) >>>> >>> >>> Then you haven't configured your environment correctly. >>> >>> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#getting-access-to-gromacs-after-installation >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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. >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
