one more question about the pull code.
I have outputted the force for pulling the molecule in .xvg file. If I pulled the molecule in Z direction, does the positive sign in front of the force mean the direction of the pulling force is identical to the positive direction of the Z axis? Fan ------------------ Original ------------------ From: "Justin Lemkul";<jalem...@vt.edu>; Date: Jul 17, 2018 To: "gmx-users"<gmx-us...@gromacs.org>; Subject: Re: [gmx-users] what is the force on the energy group when pullcode is used? On 7/17/18 6:03 AM, 1185201182 wrote: > Dear users > > > I am using the pull code to pull one of molecules in my simulation and the > molecule which is pulled is also defined as an energy group in my mdp file, > then I output the force in trr file > > > > So I wonder if the force on the pulled molecule in the trr file just includes > the force from potentials , or it also includes the force from the pull code. The forces written to the .trr are not decomposed in any way, so it's the total force acting on the atom(s) selected. Energy groups have no relevance here. -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.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.
