[gmx-users] installation_server machine_error

Vytautas Rakeviius vytautas1987 at yahoo.com
Wed Aug 23 10:26:16 CEST 2017

Well it seams that you compiled Gromacs with mpi support so now you should run it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more details.
On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, 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-----

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.

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