Thanks a lot Dr. Justin On Wed, Mar 6, 2013 at 2:52 PM, Justin Lemkul <[email protected]> wrote:
> > > On 3/6/13 7:35 AM, gromacs query wrote: > >> Dear All, >> >> How md engine in GROMACS (mdrun) detects which energy function to be used >> as it varies for different force fields (FF). Does it detects >> automatically >> from top file format, please correct me if wrong, or some other flag is to >> be provided in mdp file? e.g. CHARMM FF function and AMBER FF function >> has >> different way of handling as CHARMM FF includes Urey-Bradley term extra. >> >> > All of that information is in the topology at the force field level, which > is all packaged into the .tpr file by grompp. The use of different > function types (e.g. type 5 angles for U-B) covers most of those issues. > Other declarations in top-level force field files handle the rest > (combination rules, etc). > > -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
