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From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Tue Nov 25 2014 - 19:13:24 CST

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Hi,
During a simulation, the protein crossed the periodic box.
When analyzing the RMSD, I realized that this fact interfered in the calculation because rmsd was stable until half simulation. When protein cross the periodic border, the rmsd value abruptly increase 10 times.
I searched for similar questions in namd-list but nothing was found.
Any suggestions on how to compensate this fact?

grateful for any help

Flavio

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