[gmx-users] -pbc nojump failure

Irem Altan irem.altan at duke.edu
Thu Mar 31 00:04:10 CEST 2016


I am simulating a protein in its unit cell. I use the original .pdb file as an input, so the initial molecule is not fragmented. At the end of the simulation, I generate a .pdb file containing the trajectory of the protein as follows:

gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc nojump -o prot.pdb

Despite the fact that I use -pbc nojump, I still get all the coordinates wrapped into the unit cell, and therefore the protein fragmented. What could be wrong? (I use GROMACS 5.1.2)


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