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 What appears here is a (very) outdated version of GROMACS, and usage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