On 2/19/13 5:04 PM, Thomas Schlesier wrote:
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 input
to g_rdf.
-Justin
-------------------------------------------------------------------------------------
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?
No, I missed a piece of information in your original post. The nrexcl approach
only works with -rdf atom. I would suspect that if you want to use -rdf
mol_com, you will have to have individual groups for which you want the RDF
around the central group. You can analyze all the B groups around each A (and
vice versa, if you need to) using the -ng flag.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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