[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 1 08:28:22 CET 2009


> trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster

You might want to use -dump to extract a specific frame, rather than using -e:

trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0

Also, do mind that for a subsequent call to trjconv, using -pbc nojump
and the extracted frame as reference structure, the difference between
the dumped frame and the first in the trajectory should not be too
large. Otherwise -pbc nojump produces garbled results.



Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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