[gmx-users] Monitoring force
David L. Bostick
dbostick at physics.unc.edu
Wed Jul 9 17:20:02 CEST 2003
An alternative to hacking g_traj is just to use it one time to extract the
force on the ion from the trr file in the z dimension (i.e. use options
-nox -noy -nolen). Then use it again to extract the z-coordinate of the
ion from the trr file (again, -nox -noy -nolen). Finally modify both
xvg files and get rid of the xmgr junk in the header (i.e. get rid of
everything except the raw data and use the join unix command to create a
file containing timestamp-->col1, z-coord-->col2, and z-force-->col3.
> join coord.xvg force.xvg > z-force.dat
Beware however, if you wish to generate a PMF, good sampling becomes an
issue. No matter how well you bin the z coordinate, I am doubtful that you
will have a converged answer. Even if you constrain the ion in the z
direction and monitor it's z-force for a given value of z, it will most
likely take a while for the force to converge. Thus, you should calculate
the error bars in the force as a function of z to see if you can even talk
about any profile you get. I would reccommend umbrella sampling for this
sort of calculation as an alternative.
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On 9 Jul 2003, David van der Spoel wrote:
> On Wed, 2003-07-09 at 08:43, Semen Esilevsky wrote:
> > Dear Gromacs users,
> > Is it possible to monitor the force acting on a given
> > atom (particularly, ion) along given direction (say,
> > along Z axis)? The force should be monitored not vs.
> > time but vs. position of this atom i.e. I need a plot
> > which will show the mean force acting on atom when it
> > is situated in a given narrow slab along Z coordinate.
> > Any ideas how to implement this?
> You can store the forces in the trr file. THen it it should not be too
> hard to create a new analysis tool, or e.g. to adapt g_traj after what
> you want to get out.
> > Thank you in advance,
> > Semen
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> Groeten, David.
> Dr. David van der Spoel, Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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