Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms?
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <[email protected]> wrote: > > > On 6/12/13 5:30 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> Please, correct me if I am wrong. In ffnonbonded.itp >> >> [ atomtypes ] - these are nonbonded parameters between atoms of the same >> type >> > > No, these are the nonbonded parameters that are used when applying > combination rules between any atoms. > > > [ nonbond_params ] these are nonbonded parameters between atoms of >> different type >> > > No, these override combination rules. > > > [ pairtypes ] - 1-4 interactions >> >> If that is correct why amber force filed has only [atomtypes] column? How >> nonbonded parameters are calculated between atoms of a different type? >> The same with charmm - only [atomtypes ] and [pairtypes ] are provided. >> Would you please explain? >> >> > Gromos force fields, for instance, have complex ways of generating > nonbonded interactions that are not always the same for a given atomtype. > Other force fields just use straight combination rules and thus never need > [nonbond_params]. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
