[gmx-users] problem fitting trajectory

[Justin A. Lemkul]

I have found that the combination of -pbc mol -ur compact always looks pretty :) 
  So in addition to -fit and perhaps -center, try those two options together.

-Justin

Rebeca García Fandiño wrote:
> Hello,
> I have done a simulation using Gromacs 4 (4.0.2) and I would like to 
> have a trajectory were the protein is fitted to the first structure (to 
> mantain the exact orientation).
> 
> When I have tried
> 
> echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center 
> -fit rot+trans -pbc mol -o production_1_3_fit.xtc
> 
> visualizing production_1_3_fit.xtc I can see that the protein is fitted, 
> however there are a lot of "holes" into the water box. It seems like the 
> pbc were not correctly applied. I have tried changing a lot of options 
> (-pbc res, -boxcenter rect,...) but nothing works.
> 
> The options
> 
> trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect 
> -fit rot+trans -pbc mol -o production_1_3_fit.xtc
> 
> do not produce any hole in the box of water, but the box entirely moves 
> around the protein, and sometimes it is outside of it and not solvated.
> 
> I have also tried using Gromacs 4.0.4, but the problem is still the same.
> 
> Could anybody give an idea of how solving it, please?
> 
> Thank you very much for your help.
> 
> Best wishes,
> 
> Rebeca Garcia
> Academic Visitor
> Oxford University
> 
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-- 
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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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