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

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> 
> 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.
> 

By default, RDF is done based on atoms, so all atom-atom distances will be 
plotted as part of the RDF.  If you want a molecule-based RDF, see the options 
for the -rdf flag.

> 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).
> 

For two non-overlapping groups, this advice does not make sense.  Intramolecular 
interactions do count for the RDF calculation, though.  Perhaps you've gotten 
your advice confused?

As for the distance, have you corrected for PBC?  Are you analyzing the 
molecules that you think you are?

-Justin

> Can you please comment on this please. Your help is really appreciated.
> 
> 
> Regards,
> 
> Rob
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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