[gmx-users] unfragmenting molecule in a trajectory

Justin Lemkul jalemkul at vt.edu
Wed Feb 1 22:46:08 CET 2017

On 2/1/17 3:18 PM, Irem Altan wrote:
> Hi,
> For this I tried to do use the unfragmented configuration with the -s flag to trjconv when generating the trajectory. This results in a properly fragmented molecule, except for a single ILE residue. 3 atoms of this residue somehow remain displaced by the box size, while the other atoms of the same residue are correctly placed onto the protein. Is this a bug? If so, is there any way to circumvent it? (I use 5.1.2)

Without an exact sequence of commands, it's impossible to tell what may have 
happened.  It is extremely doubtful that trjconv has a bug in simple PBC routines.

Reconstructing "broken" molecules should be trivial with trjconv -pbc mol and a 
.tpr file passed to -s.



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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