On Fri, Oct 14, 2016 at 8:19 AM, Stregone <stregone.protonmail.com> wrote:
> radial CH3CN_N1 .1 15.0 :ACN.N
> Or that this mean that it will calculate the RDF for the mask :ACN.N to any molecule around ??
It will be from all N atoms in residues named ACN to each other. I
suggest reading the Amber 16 manual entry for cpptraj radial (29.9.57,
page 606) if you are going to be using this command.
>
> I did calculate the RDF as you suggested " :DBR :1 ", unfortunately. I got something quite strange
> #Distance_(Ang) :1_=>_:DBR
It seems that you actually used ":1 :DBR" (at least for the output you
give) since when cpptraj outputs radial data the legend order matches
the order of the masks.
> I assume that because I am studying a solvent, I must be more careful with the mask.
> therefore I did try :1.C :DBR.C, which gave me more "natural" results.
> #Distance_(Ang) :1.C_=>_:DBR.C
Note how in this output the order of the masks in the legend matches
the order of the masks you gave.
>
> Any advise that I should follow?
> Also, how do I save the average density of the calculations ?
Not sure what you mean by average density here. Output for 'radial' is
controlled by several keywords. Please read the manual entry for
'radial' in it's entirety.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 14 2016 - 07:00:02 PDT
