[gmx-users] mpirun

[Samuel Flores]

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 What appears here is a (very) outdated version of GROMACS, and usage needs to be adjusted accordingly.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