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@LIBSUFFIX@.la libgmxana@LIBSUFFIX@_la_LIBADD = libgmxana@LIBSUFFIX@_la_DEPENDENCIES = libgmxana@LIBSUFFIX@_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ libgmxana@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@LIBSUFFIX@.la \ ../gmxlib/libgmx@LIBSUFFIX@.la # link the mpi library to non-mpi names if the latter are not present install-exec-hook: libname="libgmxana@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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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-requ...@gromacs.org.
