[gmx-users] negative values of force

[Justin A. Lemkul]

Samrat Pal wrote:
> Dear All,
>               I have pulled a protein by keeping n-terminus fixed and 
> pulling the c-terminus. I tried to extract the force.xvg profile from 
> the .trr file by the following command -
> 

If you've applied the pull code, is there some reason that the pullf.xvg file 
does not contain the information you're looking for?

> g_traj -f traj.trr -s pull.tpr -of force.xvg
> 
> But in the force.xvg profile I am getting both positive and negative 
> values of force. What does it mean? Please suggest.

Simple Newtonian physics.  g_traj is extracting instantaneous forces on the 
constituent atoms, as stored in the .trr file, so all effects are considered - 
pull force, intermolecular collisions, etc.

-Justin

> Samrat 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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