Center trajectory with box dodecahedron

From: Ropon-Palacios G. (
Date: Fri Apr 16 2021 - 13:52:11 CDT

Dear users,


I am using MDanalysis to convert the DCD traj to XTC and the PDB to GRO then I use these to center the trajectory with gromacs command: "gmx trjconv -s prod.gro -f prod.xtc -o prod_center.xtc -center -pbc mol - ur compact ", when I load in VMD the GRO with the new heading, it throws me an error in bonds out of range, and when I load it with the original PSF and the XTC it does not give me this error. I would like to know if I can use the original PSF with the XTC centered to start doing analysis (type RMSD, RMSF, SASA, etc.)





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