[gmx-users] How to make a cluster whole

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 17 10:30:28 CEST 2006

Hi Chris (and others),

When doing so, be sure to use a frme which is close enough to the
starting frame in terms of the coordinates. -pbc nojump works based on
the coordinates and if you use a reference which doesn't match the
starting frame close enough everything can get really messed up.



On 10/17/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> There has been some previous discussion about how to get whole
> clusters of molecules (e.g. micelles, protein complexes) for analysis
> with tools such as g_gyrate that require unbroken molecules.
> The -pbc cluster command, although nice, doesn't always converge
> (http://www.gromacs.org/pipermail/gmx-users/2004-September/012070.html) and
> the nojump command requires that the .tpr has a whole cluster
> (something that is often not the case when using rhombic dodecahedron
> PBC).
> The following commands work together to acheive the desired result:
> 1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.9 (make sure to just
> get one frame)
> 2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr
> 3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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