[gmx-users] trjconv correct the pbc before analysis

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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