[gmx-users] improper .gro file format generated by trjconv

[Mark Abraham]

Hi,

That looks like a bug in trjconv - I presume you wrote your xtc file with
fairly low precision, and the .gro-writing routines aren't robust enough to
handle that possibility. If so, you can't fix the problem, but maybe you
can instead write to .pdb format. Also, you should be considering other
sources for your initial coordinate file, e.g. the input file you passed to
grompp, or the output coordinate / checkpoint file from the previous
equilibration stage.

Mark

On Mon, May 16, 2016 at 5:27 PM Esra Kaçar <esrakacar at iyte.edu.tr> wrote:

> Dear gromacs users;
>
> I am trying to perform micelle clustering analysis as described in gromcas
> website:
>
>    1. use trjconv
>    <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc
>    cluster to obtain a single frame that has all of the lipids in the unit
>    cell. This must be the first frame of your trajectory. A similar frame
> from
>    some previous timepoint will not work.
>    2. use grompp
>    <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp> to make
>    a new tpr file based on the frame that was output from the step above.
>    3. use trjconv
>    <http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv> -pbc
>    nojump to produce the desired trajectory using the newly produced tpr
>    file.
>
> Firstly I am trying to use trjconv to have a .gro file, but the output of
> first step gives me a .gro file in improper format, i.e.coordinates are not
> written with required spaces between each other. Here is my command line:
>
> gmx trjconv -f mytrajectory.xtc -o micelle.gro -s mytopology.tpr -e 0.001
> -pbc cluster
>
> And here is the micelle.gro file:
>
>     1CHOA   ROH    1   2.7   8.2   7.7
>     1CHOA      R1    2   3.0   8.1   7.7
>     1CHOA      R2    3   3.2   8.1   7.8
>     1CHOA   RO2    4   3.2   7.8   7.7
>     1CHOA   RO3    5   3.4   7.8   7.9
>     1CHOA      R3    6   3.4   7.8   7.7
>     1CHOA      C1    7   3.6   7.5   7.7
>     1CHOA   OCO    8   3.5   7.1   7.6
>
> What can be the possible reason for this error and how can I fix it?
>
> With regards,
> Esra
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