On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi <gianl...@u.washington.edu> wrote: > Thanks for looking into that. I wonder whether routines of libmd.so can be > called directly from a python script just like grompy calles routines from > libmdrun.so
One could do so, but the GROMACS "libraries" are not built with this kind of usage in mind, and (for example) will issue a fatal error whenever that seems right. This will also kill the calling program, which is usually unacceptable. There's a current thread on gmx-users asking about library-type functionality, too. Better behaviour isn't likely to happen until someone steps up to make the code changes. So far it's not a priority for anyone who knows the code well enough to do it, and the learning curve too daunting for everyone else! :-) One doesn't have to hit disk with output files, either. Memory-mapped files and named pipes can be useful. Mark > I wonder if I can find more documentation about this topic. > > There is a python wrapper for gromacs functions here: > > http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/ > > and a thread in the developers discussion: > > http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html > > Gianluca > > > On Sat, 31 Aug 2013, Justin Lemkul wrote: > >> >> >> On 8/31/13 3:11 PM, Justin Lemkul wrote: >>> >>> >>> >>> On 8/31/13 3:04 PM, Gianluca Interlandi wrote: >>>> >>>> I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries >>>> that I >>>> find are: >>>> >>>> libmd.so libgmxana.so libgmxpreprocess.so libgmx.so >>>> >>>> which are also produced without specifying -DBUILD_SHARED_LIBS=ON There >>>> is no >>>> library called libmdrun.so like the one used in grompy. Could it be that >>>> libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command >>>> mdrun >>>> call libmd.so? >>>> >>> >>> I have never heard of anything called "libmdrun.so" and I do not see one >>> in any >>> of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command >>> should >>> be linked against libmd.so; you can check with ldd. >>> >> >> A quick look through the GromPy documentation suggests that libmdrun.so is >> something that GromPy creates through one of its scripts. Having never used >> GromPy, that's the best I can offer. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> ================================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > ----------------------------------------------------- > Gianluca Interlandi, PhD gianl...@u.washington.edu > +1 (206) 685 4435 > http://artemide.bioeng.washington.edu/ > > Research Scientist at the Department of Bioengineering > at the University of Washington, Seattle WA U.S.A. > http://healthynaturalbaby.org > ----------------------------------------------------- > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
