[gmx-users] problem fitting trajectory

Rebeca García Fandiño regafan at hotmail.com
Wed Jun 10 20:47:10 CEST 2009

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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