<div>Manual section 4.2.13 maybe not enough. My potential functional shape is much more complex. I need at least two different force constants as C6 and C12 in LJ potential function in section 6.7.2. </div><div>I use this for block copolymer system. There is only two types of monomer(e.g. A, B) and two types of bond potential(e.g.A-A, B-B ). If I can form two tables related to the two different bond potential respectively (e.g. table 1 for A-A and table 2 for B-B), the problem will be solved. Is it possible to be done in Gromacs?</div>
<br><div class="gmail_quote">On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Jia Haitao wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello, everyone<br>
<br>
In gromacs user manual 6.7, they form non-bond potentials using table files, What should I do if I want to use a new *Bond* potential? The new bond potential combines two harmonic bond potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a standard harmonic potential.<br>
Besides, according user manual 5.7, there is 10 function types in table 5.5. How can I use the 8th and 9th type? Is there some examples? . <br>
</blockquote>
<br></div>
All the information related to what you want to do is in the manual, section 4.2.13. Per the caption of Table 5.5, bond type 8 will be used to generate exclusions (when running grompp); presumably type 9 will not. Hopefully someone will correct me if I'm wrong here.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-- <br>
*/<div class="im"><br>
Jia Haitao<br>
State Key Laboratory of Polymer Physics and Chemistry<br>
Changchun Institute of Applied Chemistry<br>
Chinese Academy of Sciences<br>
Changchun 130022, CHINA<br></div>
/*<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<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>
</font></blockquote></div><br><br clear="all"><br>-- <br><b><i><div><span style="font-weight:normal"><font face="arial, helvetica, sans-serif">Jia Haitao</font></span></div><div><span style="font-weight:normal"><font face="arial, helvetica, sans-serif">State Key Laboratory of Polymer Physics and Chemistry</font></span></div>
<div><span style="font-weight:normal"><font face="arial, helvetica, sans-serif">Changchun Institute of Applied Chemistry</font></span></div><div><span style="font-weight:normal"><font face="arial, helvetica, sans-serif">Chinese Academy of Sciences</font></span></div>
<div><span style="font-weight:normal"><font face="arial, helvetica, sans-serif">Changchun 130022, CHINA</font></span></div></i></b><br>