[gmx-users] Doubt about Steered molecular dynamics

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
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