On Thu, Sep 29, 2011 at 2:34 AM, Mariano Rech <mariano.rech.gmail.com>wrote:
> Interesting! I suggest you anyway to convert your trajectory in netcdf file
> format, or binpos, since mdcrd format is an ASCII file and in the past
> there
> were some problems with ptraj handling this format (maybe this issues have
> been fixed in the last version of ambertools but I think it is better
> having
> binary files for trajectories)
>
Those have been fixed, but the advice is still sound. NetCDF is the best
format to use for Amber trajectories for many reasons (explained on this
list many times previously).
All the best,
Jason
> Best regards
>
> 2011/9/28 Massimiliano Porrini <M.Porrini.ed.ac.uk>
>
> > My final and positive email on this subject.
> >
> > I found out that the problem might be either in the NAMD dcd
> > trajectory file format
> > or in the way trajin reads it.
> >
> > If I convert the DCD file in Amber file (mdcrd) format first and then
> > I execute the commands suggested by Niel and Carlos I get
> > a "canonical" RMSD time series (solid blue line in the attached graph):
> >
> > (1)
> >
> > trajin tetra_dyn.dcd
> > trajout tetra_dyn.mdcrd
> >
> > (2)
> >
> > trajin tetra_dyn.mdcrd
> > 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 out rmsd.dat :1-44.C,CA,N time 2
> > trajout tetra_dyn.imaged.mdcrd
> >
> >
> > And also, in displaying the imaged trajectory tetra_dyn.imaged.mdcrd,
> > this time I get the
> > whole solute (tetramer) in the middle of my truncated octahedron box for
> > the
> > entire simulation.
> >
> > Many thanks again for your helps and useful suggestions.
> >
> > Best,
> >
> >
> > Il 28 settembre 2011 12:26, Massimiliano Porrini <M.Porrini.ed.ac.uk>
> > ha scritto:
> > > Dear Carlos, Tom and Bruno,
> > >
> > > From what I understood by "playing" with my trajectory and your very
> > > useful comments I should probably increase the size of my cell
> > > (and this time I will hack the topology file so that to have only
> > > one molecule as solute).
> > >
> > > If I display the trajout imaged trajectory, at some point, I still see
> > > one monomer
> > > separated from the three other monomers, hence I assume that
> > > Tom and Bruno are right: my cell is too small.
> > >
> > > Using a cut off equal to 10 Angs I thought that a closest distance of
> 11
> > angs
> > > would have been appropriate for the physical behaviour of my system:
> > >
> > > solvateoct tetramer TIP3PBOX 11.0
> > >
> > > But apparently this box is too small.
> > >
> > > Another thing I should probably point out is that I generated the
> > trajectories
> > > with NAMD (using Amber coordinates and topology files), anyway I
> > carefully
> > > checked my settings through the following page:
> > >
> > > http://ambermd.org/namd/namd_amber.html
> > >
> > > And what I derived myself are the x, y and z values for NAMD
> > > cellOrigin keyword through
> > > these commands in VMD:
> > >
> > > % set sel [atomselect top "all"]
> > > % measure center $sel
> > >
> > > i. e. I assumed that the origin of the cell is equivalent to the
> > geometric
> > > center of my system, am I wrong in this? Could this be the problem of
> > > re-imaging?
> > >
> > > Thanks a lot for your hints.
> > >
> > > All the best,
> > >
> > >
> > >
> > > Il 27 settembre 2011 22:39, Bruno Rodrigues <bbrodrigues.gmail.com> ha
> > scritto:
> > >> What happens when you load the wrapped trajectory, like in Carlos'
> > script?
> > >> What does really happen with the solute. It can then give a good
> > indication
> > >> about what is wrong. Does one or two strands go to the next cell? Or
> > does
> > >> the system has any kind of sharp denaturation (probably not, but we
> > never
> > >> know...)?
> > >>
> > >> I've learned some stuff from my work with RMSD, and it sounds that a
> > part
> > >> of your molecule really went to the next cell. And I tell you more,
> the
> > >> distance between 2 cells is around 20-25 angstroms, which means that
> you
> > >> have a 12 angstroms solvent layer around your solute. I would say that
> > it's
> > >> too few for a 44 residues molecule. I use 12 angstroms for a 20
> > residues.
> > >> Maybe someone more experienced can tell something more.
> > >>
> > >> On Tue, Sep 27, 2011 at 6:14 PM, Carlos Simmerling <
> > >> carlos.simmerling.gmail.com> wrote:
> > >>
> > >>> to follow up on Tom's last sentence ("make it so all the molecules
> are
> > >>> together in the prmtop"), here is a bit of info on how to do it:
> > >>>
> > >>> Modify the pointers in your prmtop so that all the solute molecules
> are
> > in
> > >>> 1
> > >>> "molecule"
> > >>>
> > >>> - here is a sample prmtop for a dimer- the goal is to put both
> > monomers
> > >>> into a single "molecule"
> > >>>
> > >>>
> > >>> %FLAG SOLVENT_POINTERS
> > >>> %FORMAT(3I8)
> > >>> 830 10924 3
> > >>>
> > >>>
> > >>> -
> > >>> - this data is really in this format
> > >>>
> > >>>
> > >>> FORMAT(12I6) IPTRES, NSPM, NSPSOL
> > >>> IPTRES : final residue that is considered part of the solute,
> > >>> reset in sander and gibbs
> > >>> NSPM : total number of molecules
> > >>> NSPSOL : the first solvent "molecule"
> > >>>
> > >>>
> > >>> -
> > >>> - what you need to do is to
> > >>> - leave IPTRES alone (your solute is not changing)
> > >>> - change NSPM to match your "new" # molecules (if you make a
> > dimer
> > >>> into a single molecule, subtract 1. if you make 3 molecules
> > >>> into 1, subtract
> > >>> 2).
> > >>> - change NSPSOL the same way- subtract 1 or 2 or more,
> > depending on
> > >>> what you subtracted from NSPM
> > >>> - here is the "new" SOLVENT_POINTERS section that turns the 2
> > monomers
> > >>> in a single molecule:
> > >>>
> > >>>
> > >>> %FLAG SOLVENT_POINTERS
> > >>> %FORMAT(3I8)
> > >>> 830 10923 2
> > >>>
> > >>>
> > >>> - now for the next section to change- atoms per molecule.
> > >>>
> > >>>
> > >>> %FLAG ATOMS_PER_MOLECULE
> > >>> %FORMAT(10I8)
> > >>> 6015 6015 3 3 3 3 3 3
> 3
> > >>> 3
> > >>> 3 3 3 3 3 3 3 3
> 3
> > >>> 3
> > >>>
> > >>>
> > >>> -
> > >>> - what you want to do is combine the first two "molecules" (the
> > >>> monomers) into a single molecule.
> > >>> - change the "atoms per molecule" to combine the atoms from the
> > two
> > >>> molecules
> > >>> - in this case, 6015+6015=12030
> > >>> - move the numbers up- in this case, change the second 6015
> to
> > a 3,
> > >>> and delete the last 3 at the end of this section.
> > >>> - here is the modified section (not showing the removal of the
> > final 3
> > >>> from the end of this section- bu make sure you delete it).
> > >>>
> > >>>
> > >>> %FLAG ATOMS_PER_MOLECULE
> > >>> %FORMAT(10I8)
> > >>> 12030 3 3 3 3 3 3 3
> 3
> > >>> 3
> > >>> 3 3 3 3 3 3 3 3
> 3
> > >>> 3
> > >>>
> > >>>
> > >>> - *SAVE THIS TO A NEW FILE NAME, MAKING IT CLEAR BY THE NAME THAT
> YOU
> > >>> MODIFIED THE MOLECULE POINTERS*
> > >>>
> > >>>
> > >>> On Tue, Sep 27, 2011 at 4:55 PM, Thomas Cheatham III <tec3.utah.edu>
> > >>> wrote:
> > >>>
> > >>> >
> > >>> > > I try to resend my email that probably was not read/received.
> > >>> > > Any hint to fix my RMSD values would be really appreciated.
> > >>> >
> > >>> > There is probably not an easy way to fix. Look through the archive
> > as
> > >>> > suggested about imaging issues and try things like center only the
> > first
> > >>> > residue of each chain, etc. and imaging. Imaging based on the first
> > atom
> > >>> > rather than center of mas, etc.
> > >>> >
> > >>> > This was what prompted the question on the reflector back to you
> > about
> > >>> box
> > >>> > size / amount of solvent. Likely there is too little, so there is
> > not an
> > >>> > easy way to, by generic procedure, image the molecules back since
> the
> > >>> > periodic image may be closer than the unit cell, i.e. once it is
> > wrapped,
> > >>> > it becomes closer to its image.
> > >>> >
> > >>> > I have been meaning to write a smarter imaging routine that would
> > attempt
> > >>> > to minimize distances, however I have not done this.
> > >>> >
> > >>> > There are ways to make it so all the molecules are together in the
> > prmtop
> > >>> > which will prevent this.
> > >>> >
> > >>> >
> > >>> > --tec3
> > >>> >
> > >>> > _______________________________________________
> > >>> > AMBER mailing list
> > >>> > AMBER.ambermd.org
> > >>> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>> >
> > >>> _______________________________________________
> > >>> 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
> > >
> >
> >
> >
> > --
> > 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
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 29 2011 - 18:00:03 PDT
