[gmx-users] pbc problems

申昊 shenhao at mail.bnu.edu.cn
Wed Mar 5 07:41:27 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?
> >
> Most Gromacs programs deal with PBC with no manipulation required, some do not. 
>   g_rms needs a properly processed trajectory.
> -Justin

Thank you for your response! 
As you said, i also found the Rmsd by using -nojump or -mol is different from that without these commands. And i can not 
decide which one is more accurate. Furthermore, can you list some other parameters that need removed pbc conditions? 
such as SDF calculation ... 

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