[gmx-users] trjconv correct the pbc before analysis

[mu xiaojia]

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.


Jia
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