<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Sep 9, 2009, at 6:01 PM, Li Yang wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear GMXers:<br><br>I'm sorry to disturb you.<br><br>I have a question about the Marrink's coarse-grained model, Marrink, et al. Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B 2004, 108, 750-760.<br><br></div></blockquote>First of all you should upgrade your model to the new version of this model (the MARTINI CG model).</div><div>Marrink et al JPC/B 2007, 111, 7812-24</div><div>Monticelli et al JCTC 2008, 4, 819-34</div><div><blockquote type="cite"><div>In the Marrink's CG model, the electrostatic Coulombic potential is computed via cutoff scheme. In the original paper, the cutoff method is employed "with relative dielectric constant \epsilon=20 for explicit screening". Does it mean the parameter of force field is only customized for the cutoff method? As known that the Ewald method is better than the cutoff scheme for the long-range electrostatic interaction. I want to know whether the Ewald method is also OK for this model? How can I test it? I have simulated a similar system via two method respectively, which includes a big charged nano-scale particle (~6nm). But I find that the results of cutoff scheme are quite different from the PME's results. I don't know which one is right.<br></div></blockquote>The model per se is parameterized using epsilon=15 (new version) and a cutoff scheme.</div><div>This is what people should use, as if you change it you will alter the thermodynamics </div><div>properties of the model and thereby modify it. </div><div>Then some test have been made with PME for the electrostatic for bilayer systems.</div><div>Although some phenomenon does not appear in the same time scale the overall </div><div>properties of a bilayer are not affected significantly. If you choose to use PME </div><div>with MARTINI, you should make some test on your specific system to see whether </div><div>it affects the behavior of the model.</div><div><br></div><div>Note that PME is good at some things a cutoff scheme is bad but it introduces others</div><div>(effect of periodicity on small system, increased computational cost ..).</div><div>You should find some literature on this.</div><div><br></div><div>XAvier.</div><div><blockquote type="cite"><div><font class="Apple-style-span" color="#000000"><br></font>Another question is how to get the relative dielectric constant for a CG model. I'm not familiar with this topic, but I think it is the key of the above question perhaps. Yet, there are not some details in the original paper. In some other paper about different CG models, I don't find some information about this topic. Could someone please give me some refs about the computational details?<br><br><br>Thank you very much.<br><br>Li Yang<br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.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<br></div></blockquote></div><br></body></html>