Thank you Justin. So using nrexcl 0 or 1 (should be the same with constraints) and type 1 will allow bonded atoms to interact (vdW) with each other?
On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/11/13 10:46 AM, Steven Neumann wrote: > >> I was not sure about the fucntion type (1 or 2). Once in manual it is >> stated that function 1 is only for exclusions and another time it can be >> used to miimc bonds. Both functions are working though. Thanks anyway. >> >> > More precisely, constraints of type 1 generate exclusions between bonded > atoms within nrexcl (defined in the topology), whereas type 2 do not. > Whether or not you need the constraints to do this depends on the nature > of the force field. > > > -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
