Thanks Justin. On Tue, May 29, 2018 at 11:09 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 5/29/18 12:04 PM, Lakshman Ji Verma wrote: > >> Thanks Justin. A follow up question for my better understanding. >> >> Does it mean that with “periodic-molecules” False, the periodic images >> won’t affect interactions in the actual simulation box, whereas they will >> affect if I keep “periodic-molecules” True? >> > > No. Again, normal PBC and "periodic molecules" are different concepts. > > -Justin > > > Thanks >> Lakshman >> >> On Tue, May 29, 2018 at 10:53 AM Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 5/29/18 11:50 AM, Lakshman Ji Verma wrote: >>> >>>> What difference it will make I keep Periodic molecules option True or >>>> >>> False? >>> >>>> I read the manual but couldn’t understand more than keeping it False >>>> will >>>> be faster. >>>> >>> The "periodic-molecules" option is for use with "infinite" systems like >>> CNT, surfaces, etc. That is, the topology specifies bonds that always >>> span a periodic boundary. This option is distinct from normal PBC. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> <https://maps.google.com/?q=Virginia+Tech+Department+of+Biochemistry&entry=gmail&source=g> >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.