Re: Minimization

From: Peter Freddolino (
Date: Wed May 16 2007 - 13:48:58 CDT

Hi Rita,
you may want to start with some of the troubleshooting on the NAMD wiki
Your problem is probably caused by two bonded atoms being too far apart
from each other. Are you sure your minimization has converged prior to
starting dynamics? You're not running very many steps of it...

For your second question, you are correct in your interpretation;
however, temperature is meaningless during minimization, and should
always be reported as 0 (perhaps you could post your log file).

Rita Cassia wrote:
> Dear NAMD Users,
> I am trying to minimize a complex in a waterbox, following the same steps for previous simulations with pheophorbides.
> But, the simulation stops with the message :
> "ERROR: Margin is too small for 1 atoms during timestep 741.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> FATAL ERROR: Bad global exclusion count!"
> Another thing is: in the configuration file, I set the temperature at 0 Kelvin and , for minimization, I put
> "reinitvels $temperature"
> which I understand that, after 100 steps, the velocities and temperature should be reset to 0. But what I get is always values much bigger than 0 (at the first minimization step, I get 212 K, for example). Can someone clarify me this point?
> I am attaching the conf. file and I would appreciate a lot if someone can help me.
> Thanks in advance.
> Rita Leite

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:41 CST