[gmx-users] Gromacs in UBUNTU
Sanchaita Rajkhowa
srajkhowa18 at gmail.com
Tue May 19 06:03:57 CEST 2015
Thanks Marks
and really sorry for all trouble because of my stupid understanding...
On 18 May 2015 at 20:58, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> Use gmx_mpi solvate.
>
> You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS
> versions only because those are magically transformed into things like
> gmx_mpi pdb2gmx, to provide a year of backwards compatibility. But
> providing backwards compatibility for a new name was not really a good
> thing to do, so there is no solvate_mpi.
>
> GROMACS 5.1 will remove the old-style names without gmx prefixes, so people
> need to start getting used to using the gmx prefix (or learn to roll their
> own symlinks).
>
> Mark
>
> On Mon, May 18, 2015 at 5:19 PM Sanchaita Rajkhowa <srajkhowa18 at gmail.com>
> wrote:
>
> > 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.abraham at 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 <
> > 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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