On Wed, May 19, 2010 at 8:19 PM, Yunfen Wang <wangfen041237.163.com> wrote:
> Hi all,
> I compute the RDF , as respected , it outputs three rdf files
> rdf_carnal.xmgr rdf_standard.xmgr and rdf_volume.xmgr . But what is the
> diference of the three?
> Whicn one to map should I use in which condition?
> Thanks a lot in advance.
> wang
If I recall correctly, carnal style RDF contains un-normalized data, the
other two are normalized RDFs. The standard style RDF presumes a density
value of water unless assigned other-wise. The "volume" one is using volume
of the box to calculate the density. Anyway, detail information can be found
in the AmberTools.pdf manual and (unfortunately..) the source code of ptraj.
Best,
--
Mengjuei
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Received on Thu May 20 2010 - 01:30:04 PDT
