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

[teklebrh at ualberta.ca]

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.

First:
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  
result.xvg

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  
molecule.

Second:

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

[System]

-
[PAP]
-

[HEP]

[Ring_1]
   19   20   21   22   23   24   25   26   27   28   29   30
   32   34   37   38   39   40   42   44

[Ring_17]
  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  
result.xvg

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.


Regards,

Rob