Dear Fenghui Fan,
>I am not sure whether I understand you fully. How
>about Ptraj distance?
As I know, command "distance' is used to calculate distance between center
of mass of two groups. But in my case, I would like to calculate RDF of
water molecules around center of mass of one group.
Xioling
>
>Best regards.
>
>Fenghui Fan
>
>--- Xioling Chuang <xioling_c.hotmail.com> wrote:
>
> > Dear All,
> >
> > To calculate RDF from DNA atoms to water (oxygen
> > atom) using command
> >
> > radial filename 0.05 8.5 :WAT.O :1-20
> > closest density 0.033456
> >
> > as I understood, PTRAJ will calculate RDF based on
> > DNA surface. My question
> > is that how to calculate the RDF based on center of
> > mass of specific solute
> > atoms (e.g. center of mass of only residue 1)?
> > many thanks in advance for your suggestion.
> >
> > Regards,
> > Xioling
> >
> >
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Received on Wed Oct 18 2006 - 06:07:13 PDT
