[gmx-users] Catenation and Visualization

suniba sun.iba2 at gmail.com
Fri Apr 22 04:56:28 CEST 2016

Hello everyone
I have completed two independent 100 ns simulations of two differnt proteins in water. One is monomer and the other is trimer. Both simulations were allowed to run for 50 ns intially, after visulation, trajectories were 'correct' and then extended the simulation to 100 ns. Now after completion and catenation, when i converted the .xtc into movie.pdb using trjconv, the molecule seems broken in all the frames and i am not able to view it in cartoon style. Moreover, when i load the .pdb file of monomer or trimer in Pymol, Always two files are getting uploaded. I dont know what is the other file but it remains 'static' when i play the movie. Is this visualization problem or i madd a mistake in catenation? Can someone plz give insight
With Regards

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