[gmx-users] convert xtc to ASCII file

[Mark Abraham]

Hi,

Or probably gmx traj -s -f -n -ox will write an index group from a
trajectory to an .xvg text file. But generally one should consider other
ways to handle raw coordinates.

Mark

On Wed, Mar 23, 2016 at 7:19 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/23/16 2:15 PM, Athina Meletiou wrote:
> > Hello all,
> >
> > I've been wondering if there is a way to convert a Gromacs xtc
> trajectory to a plain text file. I've tried Openbabel as it appears to be
> possible but unfortunately it crashes without a warning. Is there maybe a
> Gromacs tool that can do the conversion?
> >
> > Also, as I'm interested in writing only the carbon atoms and not the
> hydrogens, I've looked at trjconv to see if I could at least do the
> selection of atoms using that, as it's specified in trjconv's manual that
> it can select a subset of atoms. However I've been looking at how to do
> that but I can't find it in the help menu of the program, so  I was
> wondering if it's not as straightforward as just selecting a subset of
> atoms through trjconv and maybe it can olny be done after writing a
> suitable index file?
> >
>
> Yes, this is exactly the function of an index file.  trjconv can output
> the .xtc
> contents in, e.g. a multi-frame PDB file by choosing that as the output
> type.
>
> -Justin
>
> > Any hints would be greatly appreciated :)
> >
> > Thank you all very much in advance.
> >
> > Best regards,
> > Athina
> >
> >
> >
> >
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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