[gmx-users] trjconv correct the pbc before analysis

Justin A. Lemkul jalemkul at vt.edu
Thu May 3 03:02:35 CEST 2012

On 5/2/12 8:55 PM, mu xiaojia wrote:
> Dear gmx users,
> I have a question about using the trjconv -pbc options before analyzing my
> trajectory. It's stated by Justin's tutorial that:
> "use trjconv to account for any periodicity in the system. The protein will
> diffuse through the unit cell, and may appear to "jump" across to the other
> side of the box. To account for such actions, issue the following:
> trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
> compact"
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html
>  )
> But for my system, I study the short peptides'  aggregation, I have many
> short peptides(not one or two single proteins) and waters, when I use -pbc
> nojump to treat my trajectory, it only gives me  correct  short peptides(no
> across out of the box), but the water is quite diffused. (I guess it is
> different with the tutorial since on it the protein is 1 or 2 polymers)
> So (1)how should I analyze such results if I want to study both short
> peptides(correct coordinates, no crossings) and waters(diffused and crossed
> box)?
> (2) I tried all the pbc options(even try them one after another, like mol
> first, nojump second), currently no clues of how to get both peptides and
> waters correct at the same time. Command for correct protein but incorrect
> waters'  coordinates is:
> trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump
> Thanks very much, I appreciate any suggestions.

In general:


For your system, I'd create an index group specifying a single peptide that will 
be convenient to locate in the center of the box.  Center on it using the 
-center option of trjconv.  You can do it all in one shot for simple systems of 
a couple peptides with trjconv -center -pbc mol -ur compact.

Note that these "corrections" for PBC are only necessary for visualization, not 
the analysis itself.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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