recenter atom and remove rotation (translation)

From: Lam T Nguyen (
Date: Tue Jul 29 2008 - 12:28:11 CDT


I simulate my system with PBCs. Is there any option in NAMD to recenter
the atoms after a number os running steps? Right now I don't know so I
have to recenter by using CHARMM after running finishes. It's not very
nice this way.

Also there are big jumps in RMSD graph for re-centered trajectory. I
check it using VMD and find that, there are obvious rotations (or
translations) between some dcd frames. Its strange for me because I use
zeromomentum option. Is there any zero-rotation option as well?



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