[gmx-developers] Modification of g_mdmat tool and compiling

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 16 09:00:45 CET 2009

Joshua Adelman wrote:
> I'm attempting to write a modified version of g_mdmat to do some custom 
> analysis of a simulation trajectory. Since what I'm trying to do 
> requires only slight modification of the code, I thought the easiest 
> thing to do is just copy g_mdmat.c and gmx_mdmat.c to something like 
> g_mdmat2.c and gmx_mdmat2.c and compile them in the src/tools directory 
> (as opposed to writing something from scratch given the template in 
> shared/template). I'm just having a little bit of difficulty getting the 
> modified versions compiled and was hoping someone could point me in the 
> right direction. Since the Makefile and Makefile.in are auto-generated, 
> I believe I shouldn't be modifying them directly. I tried inserting 
> duplicating the enteries in Makefile.am that reference the g_mdmat 
> files, and then rerun ./configure, but I'm not getting any instructions 
> for the 'g_mdmat2' tool in Makefile and Makefile.in.
This is exactly what you should do. Can you copy the
you need to add the gmx_mdmat2.c file to

libgmxana at LIBSUFFIX@_la_SOURCES = \
and the program to

> I'm working with gromacs-4.0.2. Any suggestions would be most appreciated.
> Josh 
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group              Lab: 510.643.2159
> 218 Wellman Hall                                Fax: 510.642.7428
> University of California, Berkeley     http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA                   jadelman at berkeley.edu 
> <mailto:jadelman at berkeley.edu>
> ------------------------------------------------------------------------------------------------------
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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