[gmx-users] reading velocity in the g_msd routine

Amit Choubey kgp.amit at gmail.com
Wed May 19 01:26:20 CEST 2010

On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel <gauravgoeluta at gmail.com>wrote:

> Hello gmx-users users :)
> I am modifying the 'g_msd' utility to be able to calculate viscosities
> using the corresponding Einstein relationship according to equation
> 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is
> similar to the mean-square displacement equation for self-diffusion
> coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy'
> where p_iy is the particle momenta in y-direction.
> So basically I need to be able to read both position and velocities
> from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and
> 'read_next_x' to read the coordinates. Can you please comment on how I
> can modify this code to read the corresponding velocities?

You could write your own little code to do that, see below for reading gro



> Any help is greatly appreciated.
> thanks,
> Gaurav
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