Hi Prof. Spoel.<br><br>First of all, sorry for sending this message directly to your personal email address. I was concerned that opening a thread like this would lead to undesired discussions on the mail list, and I choosen to avoid it. Please, forgive me for this intrusion.
<br><br>I'm writing this message because I could see on the gromacs web site that the version 4.0 is "coming to an end", if we can call it like that. I've already asked the question I will do again, but too long time ago and now we are in a completelly different circunstance here.
<br><br>The question is about the polarization model of gromacs: is it intended to include other models, like dipole moments interaction (like thole's one) or fluctuating charges in gromacs 4.0, in addition to the current charge on spring one?
<br><br>Long time ago, when I made such a question, the reason was no. I'm sorry for asking it again now, and I feel I should explain my reasons: I'm (finally) finishing my PhD now, and will probably give a try for a pos-PhD. Maybe one of but probably the "most exciting" possibility at moment for its project would be an extension of the current force-fields I've been developing and validating (soon to be published) with a polarization potential. IF everything goes ok, we would like to give a try to other potentials, like the ones mentioned, before choosing the best one for the types of systems we usually work with.
<br><br>That's basically the reason why I made such a question: if gromacs 4.0 is going to release with this potentials as options, it would be fairly easy and straight forward. If not, but there is any "movement" inside the developers section, I would join it right now just to see how thing are going (unfortunatelly, it would be impossible to begin to participate in such a project right now, exactly because the finalization of the PhD). If there is no movement for that, I would join only with
4.0 released and my "free" time back if I get my appliance accept, in order to learn a bit more about gromacs development and try to do this slice of the job by myself. ;)<br><br>Thanks a lot for your time, and please forgive me again for my "intrusion". ;)
<br><br>Sincerally yours,<br><br>Jones<br><br><div><span class="gmail_quote">On 6/23/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">Jones de Andrade wrote:<br>> Hi Mark.<br>><br>> Haven't got exactly what you said. So let me rephrase myself:
<br>><br>> The CF4 molecule doesn't have dihedrals nor intramolecular LJ and<br>> coulombic contributions.<br>><br>> What kind of contribution am I missing that makes potential energy minus<br>> bond stretching minus angle bending *different* from Lj + coulomb(SR) +
<br>> coulomb (LR) + Disp correction?<br>><br>> Thanks a lot in advance,<br>><br>> Sincerally yours,<br>><br>> Jones<br>><br>I didn't follow the whole discussion, but there are also exclusion<br>
corrections when using PME or RF.<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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