[gmx-users] trjconv center on protein

[Justin A. Lemkul]

Tomek Wlodarski wrote:
> Hi all!
> 
> I have a trajectory of simulation (protein in box of water) and I
> would like to have all the time protein in the center of the water
> box, becasue protein is drifting to the edge during simulation and I
> am calculating some properties of water arround the protein.
> I was playing with trjconv and -pbc and -center options and I menage
> to do what I wanted, however there was something bizarre for me or
> maybe I do not fully understand how this centering works....
> I noticed that the same water molecule traverse different distance
> between the same frames of simulation in the original than in
> converted trajectory...
> Why and how it is possible?
> Thank you for any suggestions and help!

Without seeing the exact command(s) you used to produce the centered trajectory, 
especially if it was a combination of some -pbc method and -center, then it's 
impossible to say for certain.  I'd venture a guess that you've simply managed 
to "correct" for water molecules jumping across boundaries or something, but 
that's just a guess, and without actual commands and the output you are 
obtaining, there's not much more to offer beyond speculation.

-Justin

-- 
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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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