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

Esra Kaçar esrakacar at iyte.edu.tr
Mon May 16 17:26:31 CEST 2016

Dear gromacs users;

I am trying to perform micelle clustering analysis as described in gromcas

   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

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,

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