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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.<div><br></div><div>I'm working with gromacs-4.0.2. Any suggestions would be most appreciated.</div><div><br></div><div>Josh <br><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Joshua L. Adelman</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biophysics Graduate Group Lab: 510.643.2159</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">218 Wellman Hall Fax: 510.642.7428</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, Berkeley <a href="http://nature.berkeley.edu/~jadelman">http://nature.berkeley.edu/~jadelman</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Berkeley, CA 94720 USA <a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------------------</div><br class="Apple-interchange-newline"></span> </div><br></div></body></html>