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