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