Any flag values returned when executing "minimize" and "run"?

From: Yinglong Miao (
Date: Mon Nov 19 2007 - 10:52:44 CST

Hi, NAMD developers and users,

In some of my simulations, I keep getting error messages like "FATAL
ERROR: Bad global exclusion count!" and "atoms moving too fast". I am
wondering whether there are flag values returned when executing
"minimize" and "run". Let's say, when these commands are executed
correctly, a flag value of 0 is returned; when above error messages
come up, a flag value of -1 is returned so that I can do something to
"guide" the simulation according to the flag value instead of just
going crashed.

If no such flag values returned in NAMD, could anybody tell me how is
the error "FATAL ERROR: Bad global exclusion count!" determined? I know
it could be due to stretched bonds, too close atoms or other unphysical
structure, but how does it work in computation? And how to analyze and
evolve the atomic structure to avoid above errors?

Any ideas and suggestions will be greatly appreciated!


Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405

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