Re: recenter atom and remove rotation (translation)

From: Roman Petrenko (
Date: Tue Jul 29 2008 - 15:58:03 CDT

why can't you just fix three atoms which are the closest to the
origin, so that the simulation will always keep them there and you'll
not have any drift.

On Tue, Jul 29, 2008 at 1:28 PM, Lam T Nguyen <> wrote:
> 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

Roman Petrenko.
Physics Department
University of Cincinnati

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