[gmx-users] Gromacs in UBUNTU
Mark Abraham
mark.j.abraham at gmail.com
Mon May 18 17:09:21 CEST 2015
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 <srajkhowa18 at 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.abraham at 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 <
> srajkhowa18 at 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.abraham at 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 <srajkhowa18 at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi
> > > > >
> > > > > actually all other commands are working fine. only when I am
> runing:
> > > > >
> > > > > ----------------------------------
> > > > > g at 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.abraham at 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 <
> > > > > srajkhowa18 at 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 <jjamesgreen110 at 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_poorasad at 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.
> > > > > > > > > --
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