[gmx-developers] reading velocity in gmx_msd.c

Gaurav Goel gauravgoeluta at gmail.com
Tue May 18 23:10:47 CEST 2010

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?

Any help is greatly appreciated.


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