[gmx-users] Re: Why RMSFs of some protein chains in my system are unreasonably large?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Fri Sep 15 11:47:54 CEST 2006

> are all the lysozymes treated as one protein? in that case it might be
a PBC artifact. try doing the rmsf per molecule (by running the program
> times) and then overlaying the result.
> are you trying to crystallize it?

Thank David. I just found that it was due to jumps in trajectory files.
I saw the animation of trajetory file and found some protein molecules
jumped from one side to the other side. Thus I produced a new trajectory
files using trjconv with option "-pbc nojump" and then calculated RMSF,
the result seems OK. So it is a little strange that g_rmsf can not
recognize some information about jumps in trajectory file. If it is,
could you repair it in the next release?
Zhongqiao Hu
Dept of Chemical and Biomolecular Engi.
National Univ. of Singapore

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