Re: [gmx-users] Problem with trjconv centering after fitting

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Re: [gmx-users] Problem with trjconv centering after fitting

Hi, Would that be the same? What happened here is that the system was first fitted. Thus, the system is rotated and any operation concerning pbc after that point will be screwed up, because the box definition does not match the system. Solution: first perform all operations involving pbc, then fi

Re: [gmx-users] Problem with trjconv centering after fitting

[EMAIL PROTECTED] wrote: 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

[gmx-users] Problem with trjconv centering after fitting

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 regio