AMBER Archive (2009)

Subject: [AMBER] nanoseconds of simulation with nscm=0

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Sun May 24 2009 - 12:20:18 CDT

I am trying to understand where center of mass translation and rotation come
form during a simulation. I came across the following threads
http://archive.ambermd.org/200705/0176.html
http://archive.ambermd.org/200601/0154.html. I have never have a simulation
start in NVE without any COM. Usually there is always some COM, and if I
understand the thread correctly this is due to accumulation of error when
integrating equations of motion. So in a nanosecond simulation the molecule
would move away until coordinates would be too big to write to file. Have
others been able to start a simulation without any COM?
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