Hi Patrick.<br><br>Just got this paper here, thanks for the indication.<br><br>This may sound like a dumb question, but: am I wrong, or the "shell model" and the "charge on a spring model" differ only by the fact that the VdW interation is also "floating aroung" in the "shell model" but not in the "charge on a spring" one?
<br><br>Thanks a lot,<br><br>Jones<br><br><div><span class="gmail_quote">On 5/21/07, <b class="gmail_sendername">Patrick Fuchs</b> <<a href="mailto:Patrick.Fuchs@ebgm.jussieu.fr">Patrick.Fuchs@ebgm.jussieu.fr</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>there's a very recent paper of the GROMOS team, where they evaluate the<br>
free energy of polarization (with the 'Charge-on-Spring' model):<br><a href="http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html">http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html
</a><br>Their code is already working, but under the GROMOS software...<br>Ciao,<br><br>Patrick<br><br>Jones de Andrade a écrit :<br>> Hi David<br>><br>> They have published a few paper on water and alcohols. The charm crew
<br>> have done a few more. Amber is actually split into two IIRC, with point<br>> dipoles as well as shell models (that means either or).<br>><br>><br>> I've found two papers for charmm polariability. But I'll only be able to
<br>> try to find it in the library or to ask for the authors tomorrow at<br>> least. But thanks for the information! ;)<br>><br>> On the other hand, I could not yet find any published material from<br>> amber using shell models. Is this only an "inside group" discussion?
<br>><br>> I think there is not a lot of difference, but shell models are easier to<br>> implement.<br>><br>><br>> I think too. In reality, there is no "visible rational reason" for this
<br>> fear of me, is more like a "feeling", so I'll try to find something more<br>> on it.<br>><br>> But I do agree that it's much likely that the shell model is much easier<br>> to implement, if not faster to execute also. :)
<br>><br>> I am working on shell models a bit (not enough...)<br>><br>><br>> Me too. Specially cause this is long terms plans (2+ years from now).<br>><br>> But thanks a lot for all information, David. Helped a lot.
<br>><br>> Sincerally yours,<br>><br>> Jones<br>><br>><br>> ------------------------------------------------------------------------<br>><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 <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>--<br>_______________________________________________________<br>Patrick FUCHS<br>Equipe de Bioinformatique Genomique et Moleculaire<br>INSERM U726, Universite Paris 7<br>Case Courrier 7113<br>2, place Jussieu, 75251 Paris Cedex 05, FRANCE
<br>Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30<br>E-mail : <a href="mailto:Patrick.Fuchs@ebgm.jussieu.fr">Patrick.Fuchs@ebgm.jussieu.fr</a><br>Web Site: <a href="http://www.ebgm.jussieu.fr/~fuchs">http://www.ebgm.jussieu.fr/~fuchs
</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 <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote>
</div><br>