[gmx-users] installation_server machine_error

[Mark Abraham]

Hi,

Please don't start new work with software that's no longer support and is
missing over four years worth of performance and correctness fixes. Some of
your problems relate to using commands that use the gmx wrapper binary,
which did not emerge until version 5.0.

Mark

On Wed, Aug 23, 2017 at 9:42 AM Kashif <kashifzamir180.mk at gmail.com> wrote:

> dear sir
> after installing gromacs on server, I could not able to run the simulation.
> It always shows "-bash: command not found".
>  when I tried to locate the pdb2gmx, it showed the path as-----
> /opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi
>
> When I run the following command by using the path as below----------- I
> got error
>
> [kashif at Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f
> 1aki.pdb -o 1AKI_processed.gro -water spce
>
> -bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory
>
> [kashif at Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb
> -o
> 1AKI_processed.gro -water spce
>
> -bash: /opt/apps/gromacs/4.6.6/bin/pdb2gmx: No such file or directory
>
>
> Although after looking into the installed gromacs bin directory
> (/opt/apps/gromacs/4.6.6/bin), I found all the packages of gromacs.......
>
> [root at Server bin]# ls
> completion.bash   g_dos_mpi          GMXRC.bash       g_sigeps_mpi
> completion.csh    g_dyecoupl_mpi     GMXRC.csh        g_sorient_mpi
> completion.zsh    g_dyndom_mpi       GMXRC.zsh        g_spatial_mpi
> demux.pl          genbox_mpi         g_nmeig_mpi      g_spol_mpi
> do_dssp_mpi       genconf_mpi        g_nmens_mpi      g_tcaf_mpi
> editconf_mpi      g_enemat_mpi       g_nmtraj_mpi     g_traj_mpi
> eneconv_mpi       g_energy_mpi       g_options_mpi    g_tune_pme_mpi
> g_anadock_mpi     genion_mpi         g_order_mpi      g_vanhove_mpi
> g_anaeig_mpi      genrestr_mpi       g_pme_error_mpi  g_velacc_mpi
> g_analyze_mpi     g_filter_mpi       g_polystat_mpi   g_wham_mpi
> g_angle_mpi       g_gyrate_mpi       g_potential_mpi  g_wheel_mpi
> g_bar_mpi         g_h2order_mpi      g_principal_mpi  g_x2top_mpi
> g_bond_mpi        g_hbond_mpi        g_protonate_mpi  make_edi_mpi
> g_bundle_mpi      g_helix_mpi        g_rama_mpi       make_ndx_mpi
> g_chi_mpi         g_helixorient_mpi  g_rdf_mpi        md.log
> g_cluster_mpi     g_hydorder_mpi     g_rmsdist_mpi    mdrun_mpi
> g_clustsize_mpi   g_kinetics_mpi     g_rmsf_mpi       mk_angndx_mpi
> g_confrms_mpi     g_lie_mpi          g_rms_mpi        pdb2gmx_mpi
> g_covar_mpi       g_luck_mpi         grompp_mpi       tpbconv_mpi
> g_current_mpi     g_mdmat_mpi        g_rotacf_mpi     trjcat_mpi
> g_density_mpi     g_membed_mpi       g_rotmat_mpi     trjconv_mpi
> g_densmap_mpi     g_mindist_mpi      g_saltbr_mpi     trjorder_mpi
> g_densorder_mpi   g_morph_mpi        g_sans_mpi       xplor2gmx.pl
> g_dielectric_mpi  g_msd_mpi          g_sas_mpi        xpm2ps_mpi
> g_dipoles_mpi     gmxcheck_mpi       g_select_mpi
> g_disre_mpi       gmxdump_mpi        g_sgangle_mpi
> g_dist_mpi        GMXRC              g_sham_mpi
>
>
> Kindly suggest me the proper commands so that I can run the simulation.
>
>
> regards
> kashif
> --
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