[gmx-users] Help on data anaysis in g_rdf and g_dist

teklebrh at ualberta.ca teklebrh at ualberta.ca
Sat Aug 28 00:20:48 CEST 2010

Dear Gmx users,

After working for quite sometime I managed to simulated almost all my  
molecules for 20ns. Thank you for all your help especially Justine.Now  
I am on last stage of analyzing my data.

I want to calculate g(r)and I used the following command

g_rdf -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 20000 -o  

Is this right and my data does not look right. For example for the  
PAP-PAP radial distribution function , My data did not converge to one  
at the end it goes all the way to zero. Which is wierd. when I made  
the index file do I need to make for each molecules in the system or I  
cann collectively get the g(r) for all the PAP molecules in the  
system. PAP-PAP RDF for individual molecues in the index file or for  
two separate g(r) is the right value to trust for g(r) of the PAP  


the distance between two polyaromatic rings. I develop a make index as  




   19   20   21   22   23   24   25   26   27   28   29   30
   32   34   37   38   39   40   42   44

  979  980  981  982  983  984  985  986  987  988  989  990
  992  994  997  998  999 1000 1002 1004

Those two rings are the the aggregates in the VMD. I indentified them  
and does the g_dist
between the two but my data looks a little bit off.

g_dist -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 20000 -o  

The value I got is big and does not look right. The diatnce is around  
3.5 nm but if they aggregate it must be a Pi-Pi stacking and should be  
around 0.5 angstrom. Somebody told me i need to develop a script to  
discard some interactions in the pair calculations but did not  
understand what he means ( less ins).

Can you please comment on this please. Your help is really appreciated.



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