On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 6/12/13 6:00 AM, Steven Neumann wrote: > >> 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? >> >> > No, please refer to the Gromacs manual for discussion on "combination > rules" and how they fit into the Lennard-Jones equation. > > -Justin > I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven > > >> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <jalem...@vt.edu> 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://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<h**ttp://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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
