[gmx-users] mpirun

Justin Lemkul jalemkul at vt.edu
Tue Nov 10 02:02:39 CET 2015



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 What appears here is a (very) outdated version of GROMACS, and usage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
>>>>>>
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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
>>>>
>>>> ==================================================
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>>>> 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

==================================================


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