[gmx-users] g_rdf

[Chris Neale]

Try "gmxcheck -f full.trr"
How many frames are in your .trr file? Why use a .trr anyway, use the .xtc instead (assuming that you save the xtc coords more often than the trr coords)

Next, try making an index file with make_ndx and adding "-n index.ndx" to your g_rdf command. It is unclear to me how you were able to select CA CA without providing an index file.

Third, take a closer look at your output and perhaps post it here. By at the zero distance, do you mean that you have 

...
@ subtitle "System-Ststem"
     0.001          <some number here>
     0.003          0
     0.005          0
     0.007          0
...

?

Fourth, look at your .trr in VMD. Perhaps the thing has collapsed?

************
 
Hi there,

I have a problem with g_rdf from version 3.3

I want to be sure, that I have crystal structure or liquid, so I used

g_rdf -f full.trr -s full.tpr
and selected System System
 or CA CA

But instead of normal radial distribution function, I got only 1 sharp
peak at the zero distance and zeros in other distances.

What I am doing wrong?