vmd-tprreader

Molfileplugin for VMD that lets me read in GROMACS tpr files, with some limitations. These limitations include:

• Only tested on single precision tpr files
• No alchemical changes were tested
• The files can't be made by a very old file generator. GROMACS versions prior to 4.0 may be too old to load.

To use, you are required to recompile VMD (or at least the molfile plugins), having placed the source files under plugins/molfile_plugin/src, and editing the Makefile in plugins/molfile_plugin. Specifically, you will need to add "tprplugin" to STATICPLUGINS, "tprplugin.so" to PLUGINS, "${ARCHDIR}/tprplugin-s.o" to ARCHIVEOBJS, and add the targets required for building:

tprplugin.so: ${ARCHDIR}/tprplugin.o
	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
${ARCHDIR}/tprplugin.o: tprplugin.C ${PLUGINAPI}
	$(CXX) $(CXXFLAGS) $(SHLDFLAGS) $(INCDIR) -c $< $(COPTO)$@
${ARCHDIR}/tprplugin-s.o: tprplugin.C ${PLUGINAPI}
	${CXX} ${SCXXFLAGS} $(INCDIR) $(DEF)"VMDPLUGIN=molfile_tprplugin" -c $< $(COPTO)$@

Now I think this is a very useful feature. It uses mostly pre-existing functions defined in Gromacs.h, with a few new functions that I needed to add. At this point, I think this is ready to be incorporated into VMD proper.

Testing

If you want to see how this works on a set of tprs, you can do the following:

make
make test

That would tell you if your tpr files are readable or not, along with some diagnostic information. Even better, if you have reasonably recent python installed, you can also test with the following:

make pythontest