[gmx-developers] Modification of g_mdmat tool and compiling

Joshua Adelman jadelman at berkeley.edu
Thu Jan 15 23:30:45 CET 2009

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.

I'm working with gromacs-4.0.2. Any suggestions would be most  


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/ 
Berkeley, CA 94720 USA                   jadelman at berkeley.edu

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