[AMBER] correct way of imaging for rdf

From: Jio M <jiomm.yahoo.com>
Date: Thu, 23 Jan 2014 08:06:19 -0800 (PST)

Hi all

I have a linear long molecule around 120 angs and am using truncated octahedron water box.
I am trying to test imaging on single restart file with cpptraj (for analysis of traj files for RMS mass weighted and radial distrubution of ions.)

When I use:

trajin test.nc
trajout test.pdb pdb

My linear molecule is out of box partially and looks "broken"! (but it is not broken if I just check the rst and prmtop in vmd)

I tried:
trajin test.nc
autoimage :253-269
trajout test.pdb pdb

253-269 are residues in one molecule and it shows nice unbroken structure though whole structure does not look (visually in vmd) in

center of octahedron, so I think its not good for RDF calculations.


1) What image processing should be done for RDF calculations and ofcourse I can use same traj for RMS analysis. I mean the molecule should be in center if RDF analysis to be done correcly.

2) Also as in ptraj I did not find 'mass' flag with cpptraj for rms calculations? can it be used in cpptraj as in ptraj

3) In section 8.9, Page number 230 AmberTools13 manual, the 'rmsd' and 'rms' are different things?

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Received on Thu Jan 23 2014 - 08:30:03 PST
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