[gmx-users] lost information box after g_cluster

Justin Lemkul jalemkul at vt.edu
Wed Apr 22 22:03:59 CEST 2015

On 4/22/15 11:18 AM, Rebeca García Fandiño wrote:
> Dear Gromacs users,
> when I use g_cluster -f trajectory.xtc -s topology.tpr -g clusters.log -cl clusters.pdb -cutoff 0.05 (...)
> the obtained file clusters.pdb does not contain any information about the box. I have tried with .gro, and also with the option of g_cluster -pbc, but the dimensions of the box are not written in any of the resultant structure.
> Does anyone know a way of avoiding lossing the dimensions of the box after doing a g_cluster analysis?

That would have to be added to the code, but I don't see a real compelling 
purpose.  Given that clusters.pdb can be either the central or average structure 
in the cluster, which box is relevant?  For the central member, that could 
probably be saved from the trajectory (but the input is not guaranteed to have 
box vectors) but for an average structure, what makes sense?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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