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

[ABEL Stephane 175950]

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

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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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End of gromacs.org_gmx-users Digest, Vol 118, Issue 94
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