[gmx-users] Doubt about Steered molecular dynamics

[Quyen Vu Van]

Hi Justin,
What if I use the reference group is the absolute position in space by
specifying pull-coord1-origin: x0 y0 z0?
How about the force on this point now?
Thanks

On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul <jalemkul at 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
>
> jalemkul at 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-request at gromacs.org.
>