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...@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@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@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@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 -- 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.