[gmx-users] autocorrelation function

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 13 11:30:49 CET 2005

On Thu, 2005-01-13 at 10:36 +0100, Jozef Hritz wrote:
> 	 Gromacs Users,
> I would like to ask one technical question, how to calculate velocity
> autocorrelation funcion for center of mass of polymer for describing
> global translation motion of polymer.
> I know that g_velacc is able to calculate velocity autocorrelation funcion
> for set of atoms defined in index file. Thus I can choose atoms of
> polymers and the resulting function is average of contribution comming
> from all atoms. However, this result contains also other contributions
> (rotation, ...) not only translation motion of polymer.
You can use g_traj to compute center of mass motion, or g_msd to compute
diffusion (mean square displacement).

> Thank You very much for help
> Jozef
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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