On 1/19/18 12:52 AM, Rakesh Mishra wrote:
Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same from umbrella sampling of puling code. If I restrain some different molecule (let C ) and give the reference molecule (let B) and pulling molecule (Let A), then I found that , when I pull molecule A in + x direction then C has immobility while molecule B is feeling opposite force w. r. t. molecule A. i. e. if molecule A is moving along + x direction then reference molecule B starts to move in - x direction. Now I want to know that in pulling code, does reference molecule and pulling molecule connected with imaginary spring, due to this newton third law is applying here.
Yes, of course. The biasing potential is applied to both species specified in the group setup; we use a convention of "pulled" and "reference" group for defining a suitable reaction coordinate, but the forces are always applied to any group involved in this process.
-Justin -- ================================================== 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.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
