[gmx-users] conversion xtc to xyz format with openbabel

Sun Feb 23 18:27:37 CET 2014

Or the TNG format, supported in upcoming GROMACS 5.0, VMD sometime soon,
and in its own API. TNG has state-of-the-art compression of coordinates
*and* good single-file metadata.

Mark

On Sun, Feb 23, 2014 at 1:35 PM, ABEL Stephane 175950
<Stephane.ABEL at cea.fr>wrote:

> Thanks Vitaly and Marks for you comments.
>
> I asked this question, because a collaborator is currently developing a
> code that uses files in xyz format as input. As you said Mark, PDB/xyz are
> not viable alternatives for analyzing data from large GROMACS (whatever
> code) trajectories, so I have suggested to him to use others formats such
> as xtc or dcd.
>
>
> --------
> Stéphane Abel, PhD
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> Bat 528 Door 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
>
> ------------------------------
>
> Message: 5
> Date: Sat, 22 Feb 2014 23:23:03 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,  Vitaly
>         Chaban <vvchaban at gmail.com>
> Subject: Re: [gmx-users] conversion xtc to xyz format with openbabel
> Message-ID:
>         <
> CAMNuMASYzqFF03Cu-oLLmM1wq5WNCCNBYJjpDoti5bV_CUbAhg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, Feb 22, 2014 at 10:16 PM, Dr. Vitaly Chaban <vvchaban at gmail.com
> >wrote:
>
> > The workaround is to "trjconv -o 111.pdb", open an editor, select a
> > block of coordinates, and paste in XYZ file.
> >
> > I also do not like PDB files from gromacs, but AFAIK many programs
> > generate such PDB files which other programs refuse to read.
> >
>
> Yes, this is problematic. PDB was in active use before it had a spec, IIRC
> :-) One problem implementing support for that in GROMACS is that you have
> to *know* the element in order to write its symol, and this is very ugly to
> support. Should we commit resources to writing and maintaining code to read
> in databases to provide an imperfect mapping from reside and atom name to
> element symbol for every supported force field? Or refuse to do editconf -f
> in.gro -o out.pdb or trjconv -f in.trr -o out.pdb unless -s the.tpr is
> supplied? Or accept that most tools probably cope with this particular
> imperfection because there's lots of old tools that implement it? Or write
> 'X' in those fields and deal with complaints from users of tools who see
> that the field is present and do not use whatever heuristics they have for
> coping with the empty field, or whose PDB-format trajectories are now twice
> as large because every ATOM line has thirty extra spaces and an X?
>
> Mark
>
>
> >
> > Dr. Vitaly V. Chaban
> >
> >
> > On Thu, Feb 20, 2014 at 12:47 PM, ABEL Stephane 175950
> > <Stephane.ABEL at cea.fr> wrote:
> > > Hello all,
> > >
> > > My apologies for these  out topic questions
> > >
> > >  Does anybody have already try to convert xtc trajectory into xyz with
> > openbabel?
> > >
> > > Btw, it seems that pdb file generated with editconf can not be read by
> > openbabel. I obtain the following error :
> > >
> > >  WARNING: Problems reading a PDB file
> > >   Problems reading a HETATM or ATOM record.
> > >   According to the PDB specification,
> > >   columns 77-78 should contain the element symbol of an atom.
> > >   but OpenBabel found '  ' (atom 1)
> > >
> > >
> > > Does anybody have a workaround?
> > >
> > > Thanks in advance
> > >
> > >
> > > --------
> > > St?phane Abel, PhD
> > > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> > > Bat 528 Door 138C
> > > Gif-sur-Yvette, F-91191 FRANCE
> > > Phone (portable) : +33 6 49 37 70 60
> > > --
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> ------------------------------
>
> Message: 6
> Date: Sat, 22 Feb 2014 21:08:17 -0300
> From: Marcelo Vanean <vanean22 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Temperature coupling
> Message-ID:
>         <
> CAD04EUaDgC8LwwaTZ_GWogc6uhU+7jpOwCo-8AKd6Z7WthNq3g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Michael Shirts, in this article is not discussed about the periodic
> perturbation method to calculate viscosity. Anyway, thank you.
>
> On Sat, Feb 22, 2014 at 7:16 PM, Marcelo Vanean <vanean22 at gmail.com>
> wrote:
> > Dr. Vitaly Chaban, I  know  that g_energy is doing all the work for me.
> > However I want to understand the concepts.
> >
> >
> > On Fri, Feb 21, 2014 at 6:38 PM, Marcelo Vanean <vanean22 at gmail.com>
> wrote:
> >>
> >> I am trying to calculate the viscosity of water (spc model) by periodic
> >> perturbation method. The manual says (manual 4.6.5, pages 169 - 170):
> "To
> >> obtain the correct value for the viscosity the generated velocity
> profile
> >> should not be coupled to the heat bath, also the velocity profile
> should be
> >> excluded from the kinetic energy" and "The heat generated by the viscous
> >> friction is removed by coupling to a heat bath". I don't understand.
> How is
> >> possible to couple the system to the thermal bath, but not the velocity
> >> profile?
> >>
> >> Thank you in advance.
> >
> >
>
>
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