I am still not clear because pdb2gmx_mpi, editconf_mpi.... commands are working very well. Although they have mpi suffix but its working as non-MPI.
Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get "gmx solvate" command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > These are not the installation steps you said you followed. Those previous > instructions were for a non-MPI build. You've done an MPI build, which > explains all your problems. Please be precise ;-) > > On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa <srajkhow...@gmail.com> > wrote: > > > definitely yes.. Then only I came to know about this "gmx solvant"... > else > > How could I? > > > > I don't know. The tool is called gmx solvate. > > my installation steps are follwoing - > > > > -------------- > > > > # tar xfz gromacs-5.0.4.tar.gz > > # cd gromacs-5.0.4 > > # mkdir build > > # cd build > > #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. > > -DFFTWF_INCLUDE_DIR=/soft/fftw333/include > > -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so > > -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF > > -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc > > -DGMX_MPI=ON -DGMX_DOUBLE=OFF > > -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON > > > > You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. > If you want the non-MPI tools (which is normal, since only mdrun works with > MPI), make and install a non-MPI build. > > Mark > > # sudo make > > # sudo make install > > # sudo make install-mdrun > > # source /usr/local/gromacs/bin/GMXRC > > > > # ls /soft/gmx504/bin/ > > demux.pl g_density_mpi g_gyrate_mpi > > GMXRC.bash g_rms_mpi g_tune_pme_mpi > > do_dssp_mpi g_densmap_mpi g_h2order_mpi > > GMXRC.csh grompp_mpi g_vanhove_mpi > > editconf_mpi g_densorder_mpi g_hbond_mpi > > GMXRC.zsh g_rotacf_mpi g_velacc_mpi > > eneconv_mpi g_dielectric_mpi g_helix_mpi > > g_nmeig_mpi g_rotmat_mpi g_wham_mpi > > g_anadock_mpi g_dipoles_mpi g_helixorient_mpi > > g_nmens_mpi g_saltbr_mpi g_wheel_mpi > > g_anaeig_mpi g_disre_mpi g_hydorder_mpi > > g_nmtraj_mpi g_sans_mpi g_x2top_mpi > > g_analyze_mpi g_dist_mpi g_lie_mpi > > g_options_mpi g_sas_mpi make_edi_mpi > > g_angle_mpi g_dos_mpi g_mdmat_mpi > > g_order_mpi g_saxs_mpi make_ndx_mpi > > g_bar_mpi g_dyecoupl_mpi g_mindist_mpi > > g_pme_error_mpi g_select_mpi mdrun_mpi > > g_bond_mpi g_dyndom_mpi g_morph_mpi > > g_polystat_mpi g_sgangle_mpi mk_angndx_mpi > > g_bundle_mpi genbox_mpi g_msd_mpi > > g_potential_mpi g_sham_mpi pdb2gmx_mpi > > g_chi_mpi genconf_mpi gmxcheck_mpi > > g_principal_mpi g_sigeps_mpi tpbconv_mpi > > g_cluster_mpi g_enemat_mpi gmx-completion.bash > > g_protonate_mpi g_sorient_mpi trjcat_mpi > > g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash > > g_rama_mpi g_spatial_mpi trjconv_mpi > > g_confrms_mpi genion_mpi gmxdump_mpi > > g_rdf_mpi g_spol_mpi trjorder_mpi > > g_covar_mpi genrestr_mpi gmx_mpi > > g_rmsdist_mpi g_tcaf_mpi xplor2gmx.pl > > g_current_mpi g_filter_mpi GMXRC > > g_rmsf_mpi g_traj_mpi xpm2ps_mpi > > > > which doesn't have that gmx commands.... > > > > On 18 May 2015 at 17:40, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > > > > Hi, > > > > > > Did you go and read the webpage that is suggested by the rest of that > > > message? > > > > > > Mark > > > > > > On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa < > > srajkhow...@gmail.com > > > > > > > wrote: > > > > > > > sorry.. > > > > > > > > I mean pdb2gmx, editconf, genion, grompp and mdrun.... even it has > > genbox > > > > but it says > > > > > > > > "This tool has been removed from Gromacs 5.0. " > > > > > > > > On 18 May 2015 at 15:38, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > > > > > Hi, > > > > > > > > > > What "other commands" are working? Please be specific, we don't > have > > > time > > > > > to spend on guesses :-) > > > > > > > > > > Mark > > > > > > > > > > On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa < > srajkhow...@gmail.com> > > > > > wrote: > > > > > > > > > > > Hi > > > > > > > > > > > > actually all other commands are working fine. only when I am > > runing: > > > > > > > > > > > > ---------------------------------- > > > > > > g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p > > topol.top > > > -o > > > > > > solv.pdb > > > > > > No command 'gmx' found, did you mean: > > > > > > Command 'gm' from package 'graphicsmagick' (universe) > > > > > > Command 'gcx' from package 'gcx' (universe) > > > > > > Command 'gmt' from package 'libgenome-perl' (universe) > > > > > > Command 'ngmx' from package 'gromacs' (universe) > > > > > > gmx: command not found > > > > > > ----------------------------------- > > > > > > > > > > > > this error is coming. > > > > > > > > > > > > ------------------------ > > > > > > "gmx solvant doesn't exist, of course, but I assume that was a > > typo!" > > > > > > > > > > > > I have all options but its not working and even it doesn't show > > like > > > > > other > > > > > > commands in the installation dir /soft/gmx504/bin/.... > > > > > > > > > > > > what else to try!! > > > > > > > > > > > > > > > > > > > > > > > > On 18 May 2015 at 13:11, Mark Abraham <mark.j.abra...@gmail.com> > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > You may need to give your normal user account read permission > to > > > that > > > > > > > directory. > > > > > > > > > > > > > > gmx solvant doesn't exist, of course, but I assume that was a > > typo! > > > > :-) > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa < > > > > > > srajkhow...@gmail.com> > > > > > > > wrote: > > > > > > > > > > > > > > > Dear all > > > > > > > > > > > > > > > > I followed the same steps to install Gromacs - 5.0.4 in > ubuntu > > - > > > > > 14.04 > > > > > > > > (64bit) and seems like things get installed but I am not able > > to > > > > get > > > > > > "gmx > > > > > > > > solvant" command. > > > > > > > > > > > > > > > > I have searched in my installation dir /soft/gmx504/bin/ and > > also > > > > > > "source > > > > > > > > /soft/gmx504/bin/GMXRC.bash" in my bashrc file. > > > > > > > > > > > > > > > > Kindly help. > > > > > > > > > > > > > > > > with regards > > > > > > > > Sanchaita > > > > > > > > > > > > > > > > On 14 May 2015 at 08:54, James Lord < > jjamesgreen...@gmail.com> > > > > > wrote: > > > > > > > > > > > > > > > > > Hi Saeed, > > > > > > > > > You don't necessarily need to install it first from Ubuntu > > > > software > > > > > > > > center > > > > > > > > > and then update it. you can directly get the latest version > > and > > > > > > follow > > > > > > > > the > > > > > > > > > instruction on gromacs website. > > > > > > > > > Quick and dirty installation > > > > > > > > > < > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC > > > > > > > > > > > > > > > > > > > > > > > > > > > > 1. Get the latest version of your C and C++ compilers. > > > > > > > > > 2. Check that you have CMake version 2.8.8 or later. > > > > > > > > > 3. Get and unpack the latest version of the GROMACS > > tarball. > > > > > > > > > 4. Make a separate build directory and change to it. > > > > > > > > > 5. Run cmake with the path to the source as an argument > > > > > > > > > 6. Run make, make check, and make install > > > > > > > > > > > > > > > > > > Or, as a sequence of commands to execute: > > > > > > > > > > > > > > > > > > tar xfz gromacs-5.0.5.tar.gz > > > > > > > > > cd gromacs-5.0.5 > > > > > > > > > mkdir build > > > > > > > > > cd build > > > > > > > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > > > > > > > > > make > > > > > > > > > make check > > > > > > > > > sudo make install > > > > > > > > > source /usr/local/gromacs/bin/GMXRC > > > > > > > > > > > > > > > > > > Cheers > > > > > > > > > > > > > > > > > > James > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, May 14, 2015 at 1:53 PM, saeed poorasad < > > > > > > s_poora...@yahoo.com> > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > Dear Gromacs users , > > > > > > > > > > Greetings .I want to install Gromacs with using of UBUNTU > > > > > software > > > > > > > > center > > > > > > > > > > . Now I want to know about updating process of this > > version > > > of > > > > > > > gromacs > > > > > > > > > > . Does it update automatically with Ubuntu ? > > > > > > > > > > Thanks for your attention .Best,Saeed. > > > > > > > > > > -- > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > -- > > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > before > > > > > > > > posting! > > > > > > > > > > > > > > > > * Can't post? 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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? 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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. > > > > > -- > > 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. > -- 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.