[gmx-users] mpirun
Elsaid Younes
elkhot at gmail.com
Tue Nov 10 16:37:29 CET 2015
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 What appears here is a (very) outdated version of GROMACS, and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!
>>>>
>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>> * 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!
>>>>
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * 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.
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
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>>>> posting!
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>>>>
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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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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