[gmx-users] bonded forces in output

Stanislav Šimko stanislav.simko at gmail.com
Sat Sep 26 18:00:08 CEST 2015

Dear gromacs users,
I'm writing my code to calculate pressure from trajectory files - from
problthat em atomic positions and forces - according to virial theorem.
Currently, I'm able to calculate the same pressure when I've got only
non-bonded forces of a small system (10 atoms with charges and LJ
parameters) centered in a big (100nm cubic) box. Hopefully, my code
should work also for smaller box where atoms can see periodic images.
The problem that I'm facing right now is that I do not know how to
obtain bonded forces from the trajectory files. E.g., for single spc
water molecule gromacs gives zero forces on all atoms, even though I
assigned them different velocities.
	to obtain forces I run:
	gmx traj -f *.trr -s *.tpr -of forces -fp
 Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
which means that there are some forces
	gmx energy -f *.edr -s *.tpr ...
So I would like to ask, if there is some way how to get bonded forces
out of the trajectory... (or rerun with some runtime parameters to
force gromacs to print bonded forces)

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