[gmx-users] mpirun
Elsaid Younes
elkhot at gmail.com
Tue Nov 10 01:59:34 CET 2015
Hi,
it gives me file input/output error 1aki.pdb.
Elsaid
On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes <elkhot at gmail.com> wrote:
> 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 What appears here is a (very) outdated version of GROMACS, and usage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
>> >>>
>> >>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> >>>
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>> >>>
>> >>> * For (un)subscribe requests visit
>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-request at 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
>> >
>> > jalemkul at 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!
>> >
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>> >
>> > * For (un)subscribe requests visit
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>>
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>> Gromacs Users mailing list
>>
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