[gmx-users] all_force.xvg

[Justin A. Lemkul]

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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-- 
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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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