Try this one:
trajin tetra_dyn.dcd
center :1-11 mass
image origin center
center :1-22 mass
image center familiar
center :1-33 mass
image center familiar
center :1-44 mass
image center familiar
image familiar
reference tetra.pdb
rms reference mass out rmsd.dat .C,CA,N time 2
On Mon, Sep 26, 2011 at 11:46 AM, Massimiliano Porrini
<M.Porrini.ed.ac.uk>wrote:
> Dear Niel and dear all,
>
> Thanks very much for the hint, but, unless I am missing something here,
> unfortunately it did not work in my case.
>
> As I think my problem is exactly the same as the one presented in the post
> suggested by Niel, I updated my script commands:
>
> trajin tetra_dyn.dcd
> center :1-11 mass origin
> image origin center familiar
> center :1-22 mass origin
> image origin center familiar
> center :1-33 mass origin
> image origin center familiar
> center :1-44 mass origin
> image origin center familiar
> reference tetra.pdb
> rms reference mass out rmsd.dat .C,CA,N time 2
>
> And as you can see from the attached graph the RMSD has slightly
> improved, but still I get those jumps at the end.
>
> Any idea of what's happening here would be really appreciated.
>
> All the best,
>
>
> Il 25 settembre 2011 16:47, Niel Henriksen <niel.henriksen.utah.edu> ha
> scritto:
> > 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Sep 26 2011 - 09:00:03 PDT
