[gmx-users] Problem with g_rdf
jalemkul at vt.edu
Tue Feb 19 23:12:35 CET 2013
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.
> Thanks for the suggestion. But it doesn't really fix the problem (or i don't get
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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