Hi,
i am running MD on a system where a protien and a small peptide chain are
placed closely. After running the simulation when i was analyzing the system, i
got a rmsd plot with numerous bumps. For creating the xtc file i tried
different options like -pbc nojump/whole etc and also -center tric, still i am
getting the rmsd plot with those bumps. Further i analysed the rmsd for the
protein and peptides seperatley which come up well.
I request all the members to please provide me guidanceor possible pathway to
solve this issue. Your help will be highly appreciated.
Amit
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