provided that pulling forces are normally selected (much) larger than the genuine forces in the simulated system, unfavorable interactions are unlikely to cause the observed effect. however, rotation is probably somehow geared by pulling energy. i looked though the movie - it is like a nice helicopter.
Dr. Vitaly V. Chaban On Tue, May 27, 2014 at 11:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/27/14, 11:25 AM, ANDRES ADOLFO ORTEGA GUERRERO wrote: >> >> Hi Dr Vitaly , >> >> First 3nm it is not half of any side, i used the external amino acids from >> the channel as a reference gruop, and 3nm is the distance from the SWCNT >> tip's to the channel, but 6nm from the COM, my box has 19 nm in Z axis, >> > > From what you describe, it sounds simply like the pulling force causes the > CNT to interact unfavorably with the protein, such that the biasing force > cannot actually move the CNT along the desired axis, instead dissipating the > force in some bizarre ways. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.