Dear Mark,
Thank you very much for the enlightment. I will look into named pipes.
This might be appropriate since I'm calling mdrun from a TCL script in
VMD.
Gianluca
On Sun, 1 Sep 2013, Mark Abraham wrote:
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
-----------------------------------------------------
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
