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

[teklebrh at ualberta.ca]

Dear Justine,

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

No, I did not correct for the PBC. How can I do that. And what is the  
purpose of that in the g_dist calculation.

Yes,

I just look at the last frame of my simulation and correctly  
identified the two residues that form aggregates using the sequence  
viewers in VMD. and I developed my index file based on these two. I  
got the residue name and check the group atoms that constitute in the  
polyaromatic ring of these two molecules and calculated the g_dist for  
ONLY those two molecules in the last 1ns.

> 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.

Yes, I understand that the choise of atom based or molecule based but  
when you said atom-atom based is that for only two molecules or the  
entire 24 molecules in the system ( means the two that form aggregates).

Thank you for you help Justine

Rob

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>
> ========================================
> -- 
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>