[gmx-users] trjconv center on protein

Justin A. Lemkul jalemkul at vt.edu
Fri May 6 01:15:44 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list