Hi, Well, who'd need control atoms? You'd just need to position it at a certain distance along a random vector. If you're talking about it as part of a water cluster or something, technically speaking it's not a hydroxide anymore :) On another note, as I mentioned before, the proton has an intrinsically ill-defined position. Please do understand that we're not jsut trying to bully you here. At some point you have to justify your model and a reviewer (which might be one of us :p) is likely to raise the same issues we're doing here.
Cheers, Tsjerk On Tue, Aug 18, 2009 at 2:47 AM, Mark Abraham<[email protected]> wrote: > Marc Charendoff wrote: >> >> Sorry for bringing up the hydroxide ion question again, but are there any >> hints as to how to place a single hydrogen on the oxygen atom? Can I somehow >> assign control atoms outside the hydroxide anion as a means of reference for >> the required ffG43a1.hdb modification? Looks like both methods to attach >> single protons need some kind of reference (control atoms). Thanks much, > > Was this ion parameterized for this (any?) forcefield? It seems quite > unlikely that a classical hydrogen-oxygen bonded pair with net negative > charge used with a classical water model could adequately model the kind of > labile hydrogen-bonding activity that these species undergo. > > Accordingly, it's not much of a surprise that GROMACS has no .hdb mechanism > for generating a hydroxide hydrogen. The only reasonable way of generating > coordinates would be by finding the most favourable electrostatic position, > which would require modification of genion, I expect. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://lists.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
