Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 2 21:59:44 CET 2011
Solomon Berman wrote:
> Hello friends,
> I'm working on a problem, and a piece of information that I need is the
> forces that are acting on each atom in the system. In looking over of the
> manual, I learned that the utility g_traj is capable of calculating the
> forces on each particle using the option -af. I believe option -of
> calculates the average force on the system versus time.
Your interpretation is backwards. The -of option plots X, Y, and Z components
of force vs. time for all the atoms in the selection. The -af option plots
averages (note the title of this file is "average forces").
> In looking at the output file all_force.xvg, I'm not clear what each column
> represents. Certainly, the first one is the number of the atom, but what of
> the other three that follow? I've tried looking through the manual, this
> board/mailing list, and the internet, to no avail.
The average force in X, Y, and Z. See the write_pdb_bfac() function in
gmx_traj.c. You can also check this yourself by running g_analyze on force.xvg,
which will print out averages that match what you will find in all_force.xvg.
> I appreciate any assistance/insight that can be offered! Happy New Year!
> Solomon Berman Chemistry Department Boston University-- gmx-users mailing
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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