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.
[EMAIL PROTECTED]
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.
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