<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>The first ting to do would be to read the later papers describing the philosophy<div>of the force field. There you'll find clear examples of how small molecules can</div><div>be parameterized. </div><div><br></div><div>This goes in two main steps: i) geometrization: define the number of beads, </div><div>bonds, angles, dihedrals to describe the molecule. ii) typography: define the </div><div>bead type to use for each bead. Both steps need to be iterated to get to the</div><div>best result. You'll need experimental data and atomistic simulations to fit</div><div>your model to.</div><div><br></div><div>Have fun,</div><div>XAvier.</div><div><br><div><div>On Mar 14, 2009, at 4:08 AM, lammps lammps wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div class="gmail_quote"> <div> <div class="h5"> <div class="gmail_quote"> <div class="gmail_quote"> <div class="gmail_quote"> <div><p>Hi MARTINI forcefield users,</p><p>I am very interesting in using the MARTINI forcefield for simulating my molecules, But I am not very familiar with it. So I hope some kind people can help me about its application.</p> <div><p>I want to know if It is suitable for the molecules of attached figures. It have TWO joint benzenes and ONE linked benzenes. If it is, what I should take care of ?</p><p>Thanks in advance.<br><br>-- <br>Wende Tian<br>Email: <a href="mailto:wende1225@gmail.com" target="_blank">wende1225@gmail.com</a><br>Tel: 025-83595329<br>Address: National Laboratory of Solid State Microstructures, <br> Nanjing University, Nanjing 210093, China<br>=======================================<br></p></div></div></div></div></div></div></div></div> <span><mo.jpg></span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>