[gmx-users] Gromacs-fda tool scalar force value sign

Yuliana Bosken ydavi002 at ucr.edu
Mon Jun 25 21:04:43 CEST 2018

Is anyone familiar with gmx-fda tool for pairwise force calculation.
My main concern is that I don't understand the positive and negative values
in the output file and the manual is somewhat confusing.
>From manual:
"*norm – the scalar is the norm of the vector and the sign is determined
based on the cosine of the*
*angle between the vector force and the vector determined by the positions
of the 2 atoms or the*
*position of the COM of the 2 residues:*
*• if it's positive, the vector force is oriented within -90 to 90 degrees
with respect to the*
*atoms/residues - considered to be same direction = attractive = negative*
*• if it's negative, the vector force is oriented within 90 to 270 degrees
with respect to the*
*atoms/residues - considered to be in opposite direction = repulsive =
So, I understand that if the cos is positive the force is attractive but
why "=negative", does it mean that the negative values in my output file
are attractive or does it mean that the energy would be negative and it
would be represented by positive force in my output file.
Please help me with that, since it is a key information that I get from
this calculations
I also have problem visualizing my output files using VMD or the fda_graph
module. I follow the instructions in manual but the fda_graph generated pdb
shows one colored lines along my water box sides and diagonals. Any links
to tutorial or more information would help.
Thank you very much

Yuliana Bosken

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