Thank you! On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com> wrote:
> 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 What appears here is a (very) outdated version of GROMACS, and usage 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. > -- 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.