[gmx-users] Problem with trjconv centering after fitting

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 28 08:53:40 CEST 2006

chris.neale at utoronto.ca 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 overlapping atoms and regions of zero density. Why is this?
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could this be the same problem as reported here:


David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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