Date: Wed Nov 26 2014 - 03:20:51 CST
Does your protein have two or more chains not covalently linked to
each other? Then it might by that
one chain is wrapped into 'another' cell while the other chain is
staying in the original cell. This would
result in a bad alignment.
Have a look at the 'wrap' command:
Hope it helps,
Quoting flavio seixas <oivalf_nix_at_remove_yahoo.com>:
> 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
-- Dr. Tillmann Utesch Institut für Chemie, Max-Volmer-Laboratorium TU Berlin, PC 14 Straße des 17. Juni 135 D-10623 Berlin Raum: TC-313 Tel. +49-(0)30-314-79386
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