<br><br><div class="gmail_quote">On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel <span dir="ltr"><<a href="mailto:gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello gmx-users users :)<br>
<br>
I am modifying the 'g_msd' utility to be able to calculate viscosities<br>
using the corresponding Einstein relationship according to equation<br>
3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is<br>
similar to the mean-square displacement equation for self-diffusion<br>
coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy'<br>
where p_iy is the particle momenta in y-direction.<br>
<br>
So basically I need to be able to read both position and velocities<br>
from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and<br>
'read_next_x' to read the coordinates. Can you please comment on how I<br>
can modify this code to read the corresponding velocities?<br></blockquote><div><br>You could write your own little code to do that, see below for reading gro format<br><br><a href="http://manual.gromacs.org/current/online/gro.html">http://manual.gromacs.org/current/online/gro.html</a> <br>
<br>amit<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Any help is greatly appreciated.<br>
<br>
thanks,<br>
Gaurav<br>
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