[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 21 10:52:00 CET 2011

Hi Evelyne,

> 1) trjconv  -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc

The option -pbc mol IIRC relates to the option for the unit cell
representation (-ur). To unbreak molecules using trjconv, you need to
have .tpr file and use the option -pbc whole.

> 2) trjconv  -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc
> if I use 1) and 2) the system gets "ripped" apart. The system is no longer a
> box but a flat disk (very funky)

This is because the jumps are removed and over time the lipids diffuse
in the plane. They've diffused quite a bit probably, smearing
themselves out over a disk.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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