Dear all,
When I look at the trajectory of my RNA implicit simulation, I find that some parts of the solute molecule are far away from the others, but they are still bonded together (with very long bonds). It happens occasionally, then back to normal quickly, and haven't disturbed the system except for the anomalous jump in RMSD. Is this is just a visual illusion, or something wrong with my simulation? I turned off the periodic boundary condition by setting ntb=0.
Thank in advance.
Best,
Yufeng
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Received on Wed May 01 2013 - 21:30:03 PDT
