[gmx-users] Problem with g_rdf

Thomas Schlesier schlesi at uni-mainz.de
Tue Feb 19 23:04:48 CET 2013

On 2/19/13 3:10 PM, Thomas Schlesier wrote:
 > Dear all,
 > I have a question regarding g_rdf.
 > My system consits of 10 disacchardids (in the following A-B, with
 > A-ring/monosaccharid and B-ring/monosaccharid) and i want to 
determine the RDF
 > (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B
 > A-A and B-B is no problem.
 > But for A-B g_rdf determines the intermolecular contribution (which i 
want) AND
 > the intramolekular contribution (which i wanted to be excluded).
 > Any (nice) ideas to solve this problem for GMX 4.0.7?
 > Long way would be to calculate each intermolecular contribution 
individual and
 > average over all. Would require some scripting :( so any better 
solutions are
 > welcome.

Create a topology with a value of nrexcl sufficient to exclude all
intramolecular interactions and create a .tpr file from it.  Use that as 
to g_rdf.



Thanks for the suggestion. But it doesn't really fix the problem (or i 
don't get it).
Ok what i have done (as an example only 3 molecules, A1 are all atoms of 
ring A of molecule 1, other stuff analogous)

Index group:
[ A ]
A1  A2  A3
[ B ]
B1  B2  B3
[ both ]
A1  B1  A2  B2  A3  B3

RDF(A-A): chose two times group A
RDF(B-B): chose two times group B
RDF(A-B): ?

If i chose group A and B i get the same result with 'nrexcel 3 or 10', 
i.e. mixing of intra- and intermolecluar A-B distances.
If i chose 'both' two-times, i get the impression the the result is the 
RDF between the whole disaccharides, i.e. A1 and B1 are recognised as 
one molecule (AB)1 and i get the RDF between:
(AB)1 - (AB)2 ; (AB)1-(AB)3 ; (AB)2-(AB)3

I tested this also with an index-file with only 1 molecule.
RDF(A-B) gives the intramolecular RDF
RDF(both) is zero, because the is only one molecule, center of mass 
distance must be zero.
This also doesn't depend on using 'nrexcel 3 or 10'

Did i made a mistake? Or any further ideas?


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