[gmx-users] new analysis in gromacs

[Justin Lemkul]

On 8/24/14, 5:10 AM, Atila Petrosian wrote:
> 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
> compile,
> -----------------------------------------------------------------------------------
> 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
> configure
> # 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             \
>      sigeps
>
>
> 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
> install-exec-hook:
>      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); \
>      fi;
>
> CLEANFILES   = *.la *~ \\\#*
>
> -----------------------------------------------------------------------------------
>
> Then what should I do?
>

Compile and install like you would any normal Gromacs distribution.  All the 
above does is add new source files to be compiled.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================