Hi Massimiliano,
Try to visualize your molecules using programs like VMD. Is your box size
large enough to hold your entire solutes after ~22ns? In other words, do
your solutes have enough numbers of water layers at that time range?
On Mon, Sep 26, 2011 at 1:18 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> I really do not want to annoy you with this subject again,
> but even with the commands suggested by Bruno Rodrigues
> it did not work (it got actually worse, as you can see
> from the attached graph, I apologise about giving personal names
> to the solid lines, but it was the best way to make it clear).
>
> Besides now I am more confused than before about the right keywords to use
> to obtain a nice RMSD time series.
>
> I am very thankful for the hints though.
>
> All the best,
>
>
> Il 26 settembre 2011 16:54, Bruno Rodrigues <bbrodrigues.gmail.com> ha
> scritto:
> > 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
> > _______________________________________________
> > 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
>
>
--
Best,
InSuk Joung
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Received on Mon Sep 26 2011 - 10:30:05 PDT
