[gmx-users] mpirun
Mark Abraham
mark.j.abraham at gmail.com
Tue Nov 10 16:43:14 CET 2015
Hi,
Read the documentation the center provides, and get SSH working. Talk to
the admins if necessary.
But for the kind of system-preparation work you are doing, as I think
Justin suggested, you will be fine using gromacs on your local machine /
laptop. You don't need the cluster until you are running mdrun for more
than a few hours :-)
Mark
On Tue, Nov 10, 2015 at 4:37 PM Elsaid Younes <elkhot at gmail.com> wrote:
> Hi,
>
> I deleted the old one and moved another one using box.com since scp
> doesn't
> work, but I got the same results.
> Any ideas?
>
> /Elsaid
>
> On Tue, Nov 10, 2015 at 3:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 11/9/15 7:59 PM, Elsaid Younes wrote:
> >
> >> Hi,
> >>
> >> it gives me file input/output error 1aki.pdb.
> >>
> >>
> > The most likely explanation is that file doesn't exist in the working
> > directory.
> >
> > -Justin
> >
> >
> > 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 What appears here is a (very) outdated version of GROMACS, and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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> >>>>>>>
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> >>>>>>>
> >>>>>> 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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> >>>>>
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> or
> >>>>>
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> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> posting!
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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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