Sorry Justin, Could you please explain in more details? Thanks On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 1/16/19 6:22 PM, Quyen Vu Van wrote: > > Hi Everyone, > > Please help me to understand about COM Pulling in gromacs? > > As I understand from Justin's tutorial, a dummy atom will be attached to > > the center of mass of Protein A through a spring with a force constant of > > 1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive > > direction of the z-axis, dummy atom will move at a constant velocity > > (pull_coord1_rate) > > The pullf.xvg file contains the force that the spring acts on the center > of > > mass of Protein A, right? > > > > In the manual of gromacs says: > > *pull_coord1_type = umbrella* > > > > > > *A harmonic potential is applied between the centers of mass of two > groups. > > Thus, theforce is proportional to the displacement * > > What is the force in the manual means? Are two groups here Protein A and > > Protein B or somewhat? > > Is there any pulling force acts on Protein B? > > The force acts on the spring, which is then interpolated onto the > specified groups. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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.