So there is no place to specify electrostatic interactions for pair interactions?
2009/7/27 Mark Abraham <mark.abra...@anu.edu.au> > Lee Soin wrote: > >> I see in the .top file generated by pdb2gmx: >> [ pairs ] >> ; ai aj funct c0 c1 c2 c3 >> >> The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. >> Do >> c2 and c3 parametrize electrostatic interactions? And what do they stand >> for >> respectively? Thanks! >> > > No, they're two pairs of VDW parameters, one pair each for two possible > states for a free-energy calculation. The tables in chapter 5 imply this, > but it is not at all obvious to a newcomer. > > Yes, use [ pairs ] directives to overrride the atomtype-based lookup. >>> That >>> will be tedious if there are many such atoms. Read parts of chapter 5. >>> >> > You should still do this. > > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- SUN Li Department of Physics Nanjing University, China
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
