Hi,<br><br>Constraints could be in the form of bond or direct constraints (often, in Gromacs, bonds are treated as constraints). As shown in <a href="http://www.gromacs.org/documentation/reference/online/top.html" target="_blank">http://www.gromacs.org/documentation/reference/online/top.html</a>, you may write top file as following:<br>
<br><pre>;<br>; Example topology file<br>;<br>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br> 1 1 no 1.0 1.0<br><br>; The force field files to be included<br>
#include "rt41c5.itp" <br><br>[ moleculetype ]<br>; name nrexcl<br>ABC 3<br><br>[ atoms ]<br>; nr type resnr residu atom cgnr charge<br> 1 A 1 ABC C1 1 0.683 <br>
2 B 1 ABC O2 1 -0.683<br> 3 C 1 ABC N3 2 -0.622<br><br>[ bonds ]<br>; ai aj funct c0 c1
1 2 1 1.000000e-01 0.1 <br> 2 3 1 1.000000e-01 0.1<br> 1 3 1 1.000000e-01 0.1</pre><br>c0 is the distance in nm. for c1, put a relative large value to make it stiff.<br><br>Yang Ye<br><br>
<div class="gmail_quote">On Tue, Dec 9, 2008 at 8:56 AM, Xin Liu <span dir="ltr"><<a href="mailto:yjqqliu@163.com" target="_blank">yjqqliu@163.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Yang Ye<br>
<br>
I can understand I need to put (3n-6) constraints to the system, but I don't know how to describe the constraints in the .itp file. Can you give me a example for the case.<br>
Thank you very much!<br>
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<font color="#888888">Xin Liu<br>
2008-12-09<br>
<br>
<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Regards,<br>Yang Ye<br>