chris.neale at utoronto.ca
Mon Jan 22 20:11:00 CET 2007
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>
Fourth, look at your .trr in VMD. Perhaps the thing has collapsed?
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?
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