<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear Eudes,</div><div><br></div><span class="Apple-tab-span" style="white-space:pre"> </span>You need to technically make it 1 "big molecule". As long as there are no bonds specified between molecule A and B. The big molecule will behave as if there are two molecules in it. I do it to dock small molecules to proteins.<div><br></div><div>Steps running Gromacs 3.3.3:</div><div><br></div><div>1) Combine molecules A and B into a big structure file (i.e. pdb or gro).</div><div>2) Edit this file, so that they are the same chain.</div><div>3) run pdb2gmx</div><div>4) Change all the residue names to MOL and change Protein_A to MOL in the top and pdb files.</div><div>5) Make sure that there is no bonds between molecule A and B in the top file. There probably won't be, but it is good to check anyway.</div><div>5) run grompp to check this file to see if it is acceptable to gromacs.</div><div>6) add distance restraints after the improper dihedrals. If you put it anywhere else, it will not work.</div><div>7) run grompp again to check this file to see if it is acceptable to gromacs</div><div><br></div><div>Other advise:</div><div>1) I would roughly dock the molecules together, so that you don't have to have such a large water box.</div><div>2) I would experiment with force constants and time constants for the distance restraints. A useful article is:</div><div><br></div><div><div>Torda, A. E., Scheek, R. M., and Gunsteren, W. F. v. (1989) Time-dependent distance restraints in molecular dynamics simulations, Chem. Phys. Lett. 157, 289-294.</div><div><br></div><div>I hope that helps. </div> <br></div><div><br></div><div><div><div>On Nov 15, 2008, at 3:58 AM, Eudes Fileti wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear gmx-users, I need to use constraints between two <br>polyatomic molecules in order to calculate PMF using free energy code. <br>Can anybody help me to use these constraints over two different molecules? <br>I ve already read something in the forum but not helped me enough.<br>(see <a href="http://www.gromacs.org/pipermail/gmx-users/2006-February/020049.html">http://www.gromacs.org/pipermail/gmx-users/2006-February/020049.html</a>). <br> bests<br>eef<br>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br> +55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a><br> _______________________________________________<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>