Steven Neumann wrote:
Dear Gromacs Users,
To avoid pbc in my trajectory file I used command:
trjconv -f md.trr -s md.tpr -pbc mol -ur compact -center -o md.xtc
I have choosen protein to be centered. Everything is ok with my protein
which does not jump and remains centered in the box. However, some of my
ligands change their place in given frame VERY rapidly... I had the
situation like this before the command above with my protein as
well which now is stable... Any suggestions please?
I posted a link earlier to the proper workflow. Dealing with protein-ligand
complexes can be tricky, since the COM of the protein may be reset to the center
of the box but the COM of the ligand is still across a periodic boundary. You
may have to center on a custom index group somewhere else in the protein or
center on the ligand itself to get a reasonable representation.
-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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