>
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
16
> times) and then overlaying the result.
> times) and then overlaying the result.
>
are you trying to crystallize it?
>David.
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?
Thanks,
Zhongqiao
Hu
Dept of Chemical and
Biomolecular Engi.
National Univ. of
Singapore
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