AW:

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Nov 26 2014 - 02:26:35 CST

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Did you wrap in VMD or in NAMD ?

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von flavio seixas
Gesendet: Mittwoch, 26. November 2014 02:13
An: Namd Mailing List
Betreff:

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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