On 03/05/12, mu xiaojia <[email protected]> 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)? > > That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes.
> > (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. > > > > If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps. Mark
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