Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning nonetheless :-)
On 10/14/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > question: are there chemical bonds between "molecules" (which you seem > to imply by stating the sites are connected by an aromatic ring). If > there are then your whole system should be considered as a single > molecule. Have you tried x2top on this? (gmx 3.3.2 only). > Yes they are. x2top wouldn't work, most atoms are redefined (two types of O with different charges, two types of C, etc. All are custom-fitted with Gaussians and GULP) I don't think treating the whole system as one molecule could work. A single "cell" of the crystall would have over 250 atoms, and I need 2x2 structure minimum, probably even bigger. But that might be last resort (after all , aren't some proteins over couple of thousand atoms?) BTW, what is the slope of GMX_performance vs. molecule_size curve ? There is one more regrouping that I am trying right now (namely having two moleculetypes: "cube-edge" and "cube-node", adding some table "LJ" in between). If this doesn't go, I am out of ideas. Thanks anyway. _______________________________________________ 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
