[gmx-users] trjconv center on protein

[Justin A. Lemkul]

Tomek Wlodarski wrote:
> 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!
> 

Are all the measurements being done in VMD, or are you using g_dist for any of 
these?  If you're using g_dist, then some of the distances may be affected by 
using your old .tpr file, wherein the protein is perhaps not centered.

If all of the measurements are being done in VMD, then I can't comment, but 
perhaps someone else can.  It might be useful to show how you're doing these 
measurements.  If you're not using g_dist, it would be interesting to see how 
the results of g_dist and VMD compare, in order to tease out the source of the 
difference.

-Justin

> Best!
> 
> tomek
> 
> 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
>> 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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> 

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

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

========================================