I'm trying to simulate a protein for 40ns after 20ns nvt and 20ns npt
equilibration, respectively. After nvt and npt equilibration steps the
protein looks fine to me. But when I analyze the trajectory file generated
after 40ns of production run, I found some unusual facts.
Half of the trajectory seems fine, then suddenly the loops and sheets of
the protein got elongated and after some time it came back to normal.
Can you please tell me is there any mistake I'm making during simulation ?
I have kept a screenshot of elongated-protein (trajectory snapshot) in the
The backbone RMSD (after production run) seems to fluctuate at the
beginning but reached some stable value after sometime and so does the
radius of gyration.
Please suggest me a way out.
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
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