recenter atom and remove rotation (translation)

From: Lam T Nguyen (lamnguyen_at_martech.fsu.edu)
Date: Tue Jul 29 2008 - 12:28:11 CDT

Hi,

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?

Thanks,

Lam

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:06 CST