[gmx-users] all_force.xvg

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!
> Best,
> Solomon Berman Chemistry Department Boston University-- gmx-users mailing
> list    gmx-users at gromacs.org 
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
> at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please
> don't post (un)subscribe requests to the list. Use the www interface or send
> it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list