[gmx-users] new analysis in gromacs

Atila Petrosian atila.petrosian at gmail.com
Sun Aug 24 11:10:37 CEST 2014

Dear gromacs users

I want to use a new code (g_vesicle_density) in gromacs being in this
address: http://md.chem.rug.nl/~mara/softa/.

There are 2 related files (g_vesicle_density.c and  gmx_vesicle_density.c).

I did following steps to use this analysis for my system:

1) I copied the files (g_vesicle_density.c and gmx_vesicle_density.c) to
the 'src/tools' directory of GROMACS.

2) I edited 'Makefile.am' to add the tool to the list of programs to
New Makefile.am is as follows:

## Process this file with automake to produce Makefile.in
# Note: Makefile is automatically generated from Makefile.in by the
# script, and Makefile.in is generated from Makefile.am by automake.

AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"

lib_LTLIBRARIES = libgmxana at LIBSUFFIX@.la

libgmxana at LIBSUFFIX@_la_LIBADD         =
libgmxana at LIBSUFFIX@_la_DEPENDENCIES   =
libgmxana at LIBSUFFIX@_la_LDFLAGS        = -version-info @SHARED_VERSION_INFO@

libgmxana at LIBSUFFIX@_la_SOURCES = \
    autocorr.c     expfit.c     polynomials.c     levenmar.c    \
    anadih.c     pp2shift.c     pp2shift.h     dlist.c        \
    eigio.c        lsq.c        cmat.c         cmat.h        \
    eigensolver.c   eigensolver.h    nsc.c         nsc.h        \
    hxprops.c     hxprops.h     fitahx.c     fitahx.h    \
    gmx_analyze.c    gmx_anaeig.c    gmx_angle.c    gmx_bond.c    \
    gmx_bundle.c    gmx_chi.c    gmx_cluster.c    gmx_confrms.c    \
    gmx_covar.c    gmx_current.c    \
    gmx_density.c    gmx_densmap.c   gmx_dih.c    \
    gmx_dielectric.c    gmx_kinetics.c gmx_spatial.c    \
    gmx_dipoles.c    gmx_disre.c    gmx_dist.c    gmx_dyndom.c    \
    gmx_enemat.c    gmx_energy.c    gmx_lie.c    gmx_filter.c    \
    gmx_gyrate.c    gmx_h2order.c    gmx_hbond.c    gmx_helix.c    \
    gmx_mindist.c    gmx_msd.c    gmx_morph.c    gmx_nmeig.c    \
    gmx_nmens.c    gmx_order.c    gmx_principal.c \
    gmx_polystat.c    gmx_potential.c    gmx_rama.c    \
    gmx_rdf.c    gmx_rms.c    gmx_rmsdist.c    gmx_rmsf.c    \
    gmx_rotacf.c    gmx_saltbr.c    gmx_sas.c    gmx_sdf.c    \
    gmx_sgangle.c    gmx_sorient.c     gmx_spol.c    gmx_tcaf.c    \
    gmx_traj.c    gmx_velacc.c    gmx_helixorient.c \
    gmx_clustsize.c    gmx_mdmat.c    gmx_wham.c    eigio.h        \
    correl.c    correl.h    gmx_sham.c    gmx_nmtraj.c    \
    gmx_trjconv.c    gmx_trjcat.c    gmx_trjorder.c    gmx_xpm2ps.c    \
    gmx_editconf.c    gmx_genbox.c    gmx_genion.c    gmx_genconf.c    \
    gmx_genpr.c    gmx_eneconv.c    gmx_vanhove.c    gmx_wheel.c    \
    gmx_vesicle_density.c           addconf.c     addconf.h    \
    calcpot.c     calcpot.h     edittop.c

bin_PROGRAMS = \
    do_dssp        editconf    eneconv        \
    genbox        genconf        genrestr    g_nmtraj    \
    make_ndx    mk_angndx    trjcat        trjconv            \
    trjorder    wheel        xpm2ps        genion        \
    anadock        make_edi    \
    g_analyze       g_anaeig        g_angle         g_bond          \
    g_bundle        g_chi           g_cluster       g_confrms       \
    g_covar         g_current    \
    g_density       g_densmap       g_dih           \
    g_dielectric     g_helixorient     g_principal \
    g_dipoles       g_disre         g_dist          g_dyndom        \
    g_enemat        g_energy        g_lie           g_filter        \
    g_gyrate        g_h2order       g_hbond         g_helix         \
    g_mindist       g_msd           g_morph         g_nmeig         \
    g_nmens         g_order         \
    g_polystat    g_potential     g_rama          \
    g_rdf           g_rms           g_rmsdist       g_rmsf          \
    g_rotacf        g_saltbr        g_sas           g_sgangle       \
    g_sham         g_sorient       g_spol        \
    g_sdf        g_spatial    \
    g_tcaf          g_traj          g_vanhove    g_velacc        \
    g_clustsize     g_mdmat         g_wham        g_kinetics    \
        g_vesicle_density.c             \

LDADD = $(lib_LTLIBRARIES) ../mdlib/libmd at LIBSUFFIX@.la \
    ../gmxlib/libgmx at LIBSUFFIX@.la

# link the mpi library to non-mpi names if the latter are not present
    libname="libgmxana at LIBSUFFIX@"; \
    nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
    libdir="$(libdir)"; \
    if echo $$libname | grep mpi >/dev/null ; then \
      (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S)
$$libname.a $$nompi.a ; exit 0); \
      (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S)
$$libname.so $$nompi.so ; exit 0); \

CLEANFILES   = *.la *~ \\\#*


Then what should I do?

Please guide me about that.

Thank you in advance.

More information about the gromacs.org_gmx-users mailing list