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! 2009/7/27 Mark Abraham <mark.abra...@anu.edu.au> > Lee Soin wrote: > >> My problem is actually as follows: >> > > Please describe in as full detail as reasonable the first time :-) > > I have three groups of atoms: A, B and C. Now I want to keep full >> interaction between A-B and A-C, but only retain the repulsive part of VDW >> interaction between B-C. I'm using the OPLS force field. It seems to me >> that >> the parameters for OPLS in the .itp files are specified for each atom, so >> is >> there any way to treat the interaction pairwise? >> > > 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. > > Probably, no force field was parameterized to reproduce whatever it is > you're trying to observe. > > > 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
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