Hi All
I have read papers reporting RDF calculations e.g. N-Cl which is RDF of Cl- ions around N atoms. In cpptraj I am using:
radial rdf_Cl 0.1 10 :Cl- :1-339.N volume
I have following queries:
1) Is this making spherical shells, (n1 to n) depending on 'dr' chosen (here 0.1), around each N atom and finally averaging each shell coressponding to each N (average all n1 for all Ns, average of n2 for all Ns and so on....)?
2) Also does the spherical shell cross the original box as well? Which I think yes as I have some N atoms at one corner of the box so the rdf should cross the boundry.
3) Is there any function any one knows that helps for linear molecules. eg. if I use
radial rdf_Cl 0.1 10 :Cl- :1-339 volume (Note not considering N atoms in mask2)
then it will consider center of mass of 1-339 resdiues and make spherical shells around center of mass, which would not be a good representation. So is there something cylindrical distribution function in cpptraj?
thanks
Jiom
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 17 2014 - 12:30:02 PDT
