[gmx-users] mpirun
Elsaid Younes
elkhot at gmail.com
Mon Nov 9 19:20:29 CET 2015
Thank you!
On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelfloresc at 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 <jalemkul at 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 What appears here is a (very) outdated version of GROMACS, and usage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 at 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 <jalemkul at 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
> >>>
> >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>
> >
> > --
> > ==================================================
> >
> > 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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
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> posting!
> >
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