<div dir="ltr">grompp accepts the index file and does all of the checking - mdrun just gets a vector of 0 or 1 in the .tpr file according to which atom is in which type of group. You should not need to get involved there, though, because the .mdp options user1-grps and user2-grps are intended to suit what your purpose sounds like. grep for User1 and cU1 to see how to get at the resulting data structures.<div>
<br></div><div>Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 26, 2013 at 2:44 PM, Jheng Wei Li <span dir="ltr"><<a href="mailto:lijhengwei@gmail.com" target="_blank">lijhengwei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hello, all<br></div> I am passing an index file chopping atoms into several subgroups, and <br>
</div>I want to utilize this information in minimize.c! <br></div>How do I recall index information in minimize.c?<br>
Please give me some advice or which part of code should I take a look to mimic its format!<br><br></div><div>JhengWei Li<br><span><font color="#888888">Institute of Atomic and Molecular Sciences,<br>
Academia Sinica, Taipei 106, Taiwan</font></span><br></div></div>
<br>--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
</blockquote></div><br></div>