<p dir="ltr">Both of those should be done in a script before calling grompp! There is not yet enough reason to bother with the complexity of modifying initial coordinates inside mdrun.</p>
<p dir="ltr">Mark</p>
<div class="gmail_quote">On Nov 28, 2013 6:27 AM, "Jheng Wei Li" <<a href="mailto:lijhengwei@gmail.com">lijhengwei@gmail.com</a>> wrote:<br type="attribution"><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><div><div>Thank you to clarify my question, Anton.<br></div> In do_lbfgs that I am currently modifying,<br></div>the information I need to provide at first place is about xx & ff.<br>
</div> My intention now is adjusting the coordinates before going into the main loop,<br></div>like swap the xyz between two atoms which are different species, or, later, <br></div>my adviser want to identify a molecule and rotate it before doing the minimization.<br>
</div> Therefore, the first thought I jump out is reading the index or atomtype, but it looks not trivial to me...<br>JhengWei Li<span><font color="#888888"><br>Institute of Atomic and Molecular Sciences,<br>Academia Sinica, Taipei 106, Taiwan</font></span><br>
<div><div><div><div><div><div><br><br></div></div></div></div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Nov 27, 2013 at 11:33 AM, 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>Uhhh.. add something ...<br></div><div>After all, I just need to divide the system into some subgroups, <br>
</div><div>I just want to call it and I don't need to change it!<br> <br></div></div><div><div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, Nov 27, 2013 at 11:28 AM, 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>Thank you, Mark.<br></div>Or could I find a way to recall the atomtype?<br></div><div>Will that be easier?<div><br><br>JhengWei Li<br><span><font color="#888888">Institute of Atomic and Molecular Sciences,<br>
Academia Sinica, Taipei 106, Taiwan</font></span><br></div></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 26, 2013 at 9:44 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>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>
</div></div></blockquote></div><br></div>
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