[gmx-users] problem with trjconv

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 3 13:13:20 CET 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi all,
> I am trying to use *trjconv command for -pbc but POPC molecules are breaking
> when visualize in VMD. The commands  used are
> grompp -f  pr.mdp  -c  em_out.gro -p .top -n index.ndx -o out.tpr
> trjconv  -f em_out.gro  -s out.tpr  -o trj_out.gro  -pbc inbox or cluster or
> whole

Your scheme will not work because the structure in the .tpr file is the same as
in your em_out.gro, which you claim to be broken.  I'm assuming em_out.gro
refers to your structure following energy-minimization?  And if so, I'm
wondering what you've done that's left a broken molecule following EM.  Is your
em_out.gro whole?


> Thi trj_out.gro contain broken POPC molecules
> Pls suggest me what options I have to use for -pbc? or any addition option I
> have to use?
> Thanks in advance.......


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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