Minimization

From: Rita Cassia (Rita.Cassia_at_gmx.de)
Date: Wed May 16 2007 - 12:19:51 CDT

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

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