[gmx-users] autocorrelation function

[David van der Spoel]

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
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++