The Amber mailing list archive is a great resource to search:
http://archive.ambermd.org/
It so happens that this issue has been discussed numerous times.
It is an imaging issue ... this post explains what to do nicely:
http://archive.ambermd.org/201103/0607.html
If you search the archive there are lots of examples and a few
different approaches to dealing with it.
Good luck,
--Niel
________________________________________
From: Massimiliano Porrini [M.Porrini.ed.ac.uk]
Sent: Sunday, September 25, 2011 9:22 AM
To: AMBER Mailing List
Subject: [AMBER] fixing rmsd values
Dear all,
I have worked out the rmsd time series for a 30 ns trajectory
of my system, which is a tetramer of a 11-residues peptide
in explicit water, using the following ptraj commands:
trajin tetra_dyn.dcd
center :1-44 mass origin
image :1-44 origin center
reference tetra.pdb
rms reference mass out rmsd.dat .C,CA,N time 2
As you can see from the attached graph the rmsd time series bears
some "jumps".
These are due to the fact that the center of mass of one or more monomers
exceeds the boundaries of my cell (truncated octahedron) during the
simulation and
generate the high values of the RMSD.
Does anybody know how I might fix the RMSD values via any ptraj commands?
Any suggestion would be really appreciated.
Best,
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Sun Sep 25 2011 - 09:00:03 PDT
