[gmx-users] trjconv center on protein

Tomek Wlodarski tomek.wlodarski at gmail.com
Fri May 6 17:14:33 CEST 2011

Dear Justin,

Thanks, sure I will give more details.

This command I've used for trajectory conversion:

trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr

Then I was analysing a new and old trajectory in VMD with my own script.
I have noticed that in old trajectory water234 between frame 0 and 1
moves 1.2089872880760837 A, whereas the same water molecule between
the same frames but in the new trajectory moves 1.4933788404331632 A
I check different water - water236 and situation was similar: old
trajectory -> 0.6436778227352694 A and in new trajectory it was
0.2921395545132566 A

So after trajectory conversion water displacement is different,
sometimes in the new trajectory is bigger and sometimes is smaller
that it was in old one...

I used the same conversion for part of my simulation where protein was
in the center of the system, and results were similar.

I believe is not problem with my vmd script because even when I open
in the same window new and old trajectory in VMD I can see "by eye"
the difference of water movement....
I am missing something?
Thanks for any suggestions and help!



On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> 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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