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.
-Justin
I appreciate any assistance/insight that can be offered! Happy New Year!
Best,
Solomon Berman Chemistry Department Boston University-- gmx-users mailing
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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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