[gmx-users] where're all the tools gone .. ?

Justin Lemkul jalemkul at vt.edu
Wed Sep 28 15:48:35 CEST 2016

On 9/28/16 9:35 AM, Frank Eisenmenger wrote:
> When compiling gromacs 5.1.4, after
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs51
> make & sudo make install, /usr/local/gromacs51/bin/ contains, ONLY:
>   demux.pl, gmx, gmx-completion.bash, gmx-completion-gmx.bash
>   GMXRC, GMXRC.bash, GMXRC.csh, GMXRC.zsh, xplor2gmx.pl
> But, by 'making' gromacs 4.6.7, I get MANY MORE in <path>/gromacs46/bin/
> completion.bash  eneconv    g_bond       g_covar       g_dipoles genbox
> g_filter       g_hydorder  g_mindist  GMXRC.bash g_options    g_protonate
> grompp    g_select   g_spol      g_wham mdrun_mpi  trjorder
> completion.csh   g_anadock  g_bundle     g_current     g_disre genconf
> g_gyrate       g_kinetics  g_morph    GMXRC.csh g_order      g_rama
> g_rotacf  g_sgangle  g_tcaf      g_wheel mk_angndx  xplor2gmx.pl
> completion.zsh   g_anaeig   g_chi        g_density     g_dist g_enemat
> g_h2order      g_lie       g_msd      GMXRC.zsh g_pme_error  g_rdf
> g_rotmat  g_sham     g_traj      g_x2top pdb2gmx    xpm2ps
> demux.pl         g_analyze  g_cluster    g_densmap     g_dos g_energy
> g_hbond        g_luck      gmxcheck   g_nmeig g_polystat   g_rms
> g_saltbr  g_sigeps   g_tune_pme  make_edi tpbconv
> do_dssp          g_angle    g_clustsize  g_densorder   g_dyecoupl genion
> g_helix        g_mdmat     gmxdump    g_nmens g_potential  g_rmsdist
> g_sans    g_sorient  g_vanhove   make_ndx trjcat
> editconf         g_bar      g_confrms    g_dielectric  g_dyndom genrestr
> g_helixorient  g_membed    GMXRC      g_nmtraj g_principal  g_rmsf
> g_sas     g_spatial  g_velacc    mdrun trjconv
> How can I build all those tools for gromacs 5.1.4, too ?

You did.  Everything is one program, called gmx.  Please consult the manual, 
release notes, mailing list archive (this gets asked probably once a week, 
despite being announced several times since version 5.0 a few years ago) and 
available tutorials for all the changes, updated syntax, etc.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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