[gmx-users] Problem with trjconv centering after fitting

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Aug 27 22:29:46 CEST 2006

Starting from a rhombic dodecahedron xtc file,

trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc
trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc

Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless,
a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this?

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