Hi Prof. Spoel. 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.
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. 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? 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. 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. ;) Thanks a lot for your time, and please forgive me again for my "intrusion". ;) Sincerally yours, Jones On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Jones de Andrade wrote: > > Hi Mark. > > > > Haven't got exactly what you said. So let me rephrase myself: > > > > The CF4 molecule doesn't have dihedrals nor intramolecular LJ and > > coulombic contributions. > > > > What kind of contribution am I missing that makes potential energy minus > > bond stretching minus angle bending *different* from Lj + coulomb(SR) + > > coulomb (LR) + Disp correction? > > > > Thanks a lot in advance, > > > > Sincerally yours, > > > > Jones > > > I didn't follow the whole discussion, but there are also exclusion > corrections when using PME or RF. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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