[gmx-users] remove periodic boundary in tpr file

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 4 11:25:36 CEST 2007


I try to remove the periodicity

You don't remove periodicity. -pbc nojump removes jumps due to (over) the
PBC, not the PBC itself.

to get a new .xtc file and one .gro
> file. The commands are shown below:
> "trjconv -f original.xtc -s original.tpr -n index -o frame_0.gro -dump 0
> -pbc nojump"

Since your frame_0  will hold the same coordinates as your .tpr file, -pbc
nojump serves no purpose here.

"trjconv -f original.xtc -s original.tpr -n index -o new.xtc  -pbc
> nojump"
> When I use g_rms to calculate the rmsd by new .xtc and .gro file, there
> is a warning and other things goes well. Command i used is "g_rms -f
> new.xtc -s frame_0.gro -o  rmsd.xvg" and the warning is "can not make
> broken molecules whole without a run input file,don't worry, mdrun
> doesn't write broken molecules". I think i have removed the boundary,
> and why it says there is an broken protein?

It doesn't say there's a broken molecule. It says it couldn't fix one if it
were present, because you don't provide topology information. But it also
says that an .xtc file generated by mdrun (and not otherwise processed)
doesn't contain broken molecules.


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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