[gmx-users] trjconv correct the pbc before analysis

[Mark Abraham]

On 03/05/12, mu xiaojia <muxiaojia2010 at gmail.com> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120503/af80dc93/attachment.html>