[gmx-users] Visualization of trajectories in PyMol

Maurício Menegatti Rigo mauriciomr1985 at gmail.com
Thu May 13 00:24:59 CEST 2010


I'm performing a 10 ns molecular dynamics of a homodimer, using GROMACS. I
have no problems during and after the simulation, since I have already
analyzed the log files and performed the checking. I was able to see,
without any problems, the whole concatenated trajectory file with VMD
software. However, when I tried to visualize with PyMol, occurs some
problems in the last frames, like wrong bonds and dismantlement of my dimer.
I'm already use the parameters *-pbc mol* and *-pbc nojump* with trjconv.
Any idea?

Thanks in advance,

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