Dear Amber users,
I am analysing a solvent box simulation using cpptraj.
At the moment I am dealing with a functions called radial, with allow the calculation
of radial distribution function (rdf).
Unfortunately I do not have enough experience using cpptraj, so I would like to
confirm that my script is correct, cause I am getting some estrange results. Unfortunately, I did not find answer in the AMBER mail list regarding to my issue.
# script
parm prmtop
trajin mdcrd
radial r.rdf 0.1 15 :1 :DBR volume center1
(this is for calculating the rdf from the residue 1[mask1] to any DBR [mask2] residue)
radial ra.rdf 0.1 15 :1.C:DBR volume
(if I understood correctly, this is for finding from the C atom in the residue 1, atom that belong to DBR residue)
radial radi.rdf 0.1 15 :1:DBR volume center1
go
the descriptions of the lines are correct ?
is there any difference between the 1st and the 3rd commands?
Thanks in advance
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Received on Wed Oct 12 2016 - 16:00:02 PDT
