[gmx-users] Gromacs in UBUNTU
Mark Abraham
mark.j.abraham at gmail.com
Mon May 18 17:28:34 CEST 2015
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.
> > > > > > > > > > > --
> > > > > > > > > > > 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list