[gmx-users] mpirun

[Justin Lemkul]

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What appears here is a (very) outdated version of GROMACS, and usage needs to be 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

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