CoM motion not removed

From: Neema Salimi (nsalimi9_at_itsa.ucsf.edu)
Date: Wed Feb 18 2004 - 13:00:22 CST

Next message: Gengbin Zheng: "Re: Running AIX version of NAMD on IBM cluster"
Previous message: Wei Fu: "atom numbers limitation"
Next in thread: Jim Phillips: "Re: CoM motion not removed"
Reply: Jim Phillips: "Re: CoM motion not removed"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

('binary' encoding is not supported, stored as-is) When doing a simulation with a protein fixed and surrounded by solvent, I have
noticed that CoM motion is not removed at the beginning of the simulation.
However, in the same system, when the protein is not fixed, the CoM motion is
removed. In addition, the values of the momenta written out by NAMD are much
larger for the fixed protein system than the unfixed protein system. How
can I fix
this?

Neema Salimi
nsalimi9_at_itsa.ucsf.edu
Graduate Student - Agard Laboratory
Program in Biophysics
University of California, San Francisco

Next message: Gengbin Zheng: "Re: Running AIX version of NAMD on IBM cluster"
Previous message: Wei Fu: "atom numbers limitation"
Next in thread: Jim Phillips: "Re: CoM motion not removed"
Reply: Jim Phillips: "Re: CoM motion not removed"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:21 CST