[gmx-users] rdf / sdf around a specific point

[chris.neale at utoronto.ca]

> if i didn't overlooked sth, g_rdf and g_sdf are calculating the  
> function around an atom or a set/com of a set of atoms. Is there an  
> easy way to calculate the functions around a specific coordinate?

I wrote a g_sdf program that works on absolute coordinates. For my  
usage, I usually want the standard implementation and I therefore fit  
my trajectory based on the atom or a set/com first and then run g_sdf.  
A straight usage of this program should give you what you want. The  
output is gaussian98 cube format for display. You would need to do  
your own integration if you wanted an rdf. The only tricky part will  
be that you will probably need to trjconv your trajectory to put your  
desired coordinate center at the center of the box or at some regular  
spacing with respect to your g_sdf chosen bin width such that for  
example the tenth box in the x direction is exactly the same distance  
from your coordinate as is the tenth box in the negative x (and  
y/z/etc.) direction.

Send me an email off-list if you want me to send you a copy.
chris.neale at utoronto.ca

I will post it but I don't know how to do that except by posting code  
directly to this list. I have previously posted it to this list here:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023641.html
Please be sure to note that although the first link in that email is  
the code, there are two more links that are important (a bug fix and a  
modified method of usage) -- Although the method of usage that is  
posted will clearly not apply to your case.