AMBER Archive (2001)

Subject: rigid body motion

From: dkon_at_email.arizona.edu
Date: Mon Jul 23 2001 - 12:20:27 CDT

Hello,

First, thank you to Carlos Simmerling and Hai Long for helping me with my
last query. I have another one that I can't figure out from the resources.

It seems that during the simulation my protein travels a lot (all the
atoms move by something like 30 A). However, it is a periodic box simulation,
and when I view the trajectory graphically, I don't see protein rotating
or traslating. Is this an imaging issue? Or do I need to take out rigid-body
motion? I couldn't find such an option in either ptraj or carnal.

I know about NSCM option, but it doesn't work for periodic boundaries,
I don't know why. Any advice would be greatly appreciated.
Best,
Dmitry.