[gmx-users] pbc problems

申昊 shenhao at mail.bnu.edu.cn
Wed Mar 5 03:08:52 CET 2014

Hello everyone!

I am a new one of gromacs. When a simulation of protein in water is finished, should i first use the command of trjconv to remove pbc conditions(with nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some other parameters)? Is the result believable without removing the pbc conditions or it is necessary for some specific calculations?

Thank you very much!

 Hao Shen

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