[gmx-users] regarding pbc issue

Justin Lemkul jalemkul at vt.edu
Wed Jan 17 13:49:47 CET 2018

On 1/17/18 5:51 AM, Vidya R wrote:
> Hi Justin,
> I got the same result as you said.
> What confused me was,  when I viewed movie.pdb file generated by the
> following command,
>   gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 10000.0 -n
> index.ndx -o movie.pdb
> two hydrogen molecules of my organic compound, were unbonded to my molecule
> (which is not supposed to be).  They are far away from molecules (their
> bonds were broken)
> Is it a pbc problem?
> Because, when I used
> gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
> gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
> gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc
> and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Making molecules whole should always be the first step. If you try to 
remove jumps with "broken" molecules, what you visualize will be 
garbage. A separate issue is with respect to the analysis programs - 
many are PBC-aware and can handle the original trajectory without 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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