[gmx-users] negative values of force

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 14 19:34:25 CEST 2010

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.


> Samrat 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list