[gmx-users] Query

[amit upadhyay]

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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