How to get around with "atoms moving too fast"

From: Yinglong Miao (
Date: Fri Oct 19 2007 - 11:45:50 CDT

Hi, NAMD developers and users,

I am introducing a new method into NAMD to accelerate MD simulations.
For the protein system in vacuum I have been testing, it works out well
for the direct MD simulations by following minimization of the initial
PDB structure, thermalization and finally a MD product run.

But I have been getting error messages, like "FATAL ERROR: Bad global
exclusion count!" and "atoms moving too fast", when implementing my
method. The method for accelerating MD involves a set of simulation
cycles, in which a few number of MD time steps are run first, then with
the output structure from MD run we apply some mathematical functions
to atomic coordinates to get a new configuration and put it back to the
MD run as input to start another cycle. Depending on the parameters and
functions I use to generate the new configuration, the simulation can
be done for as many cycles as I want, but can also crash with the above
error messages after several cycles when the configuration generated is
too strange with long stretched bonds, too close atoms, etc.

So I am wondering whether I can make the atom velocity limit larger in
NAMD to get around the error or run an additional MD run with a smaller
timestep after getting the new configuration. But it seems I can set
only one timestep in NAMD configure file. Is there a way to set
different timesteps for multiple MD runs?
And are there any other NAMD techniques I can make use of to tackle my
problem? Your comments and suggestions are 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:24 CST