Gradient tolerance nan for A three-atom simulation

From: accomp lin (
Date: Mon Jan 05 2009 - 23:09:41 CST

Dear NAMD developer:
I've modifed a namd source code with New bond energy potentials for my Coarse Grained models. After I recompiled it successfully on linux, I constructed a three-atom model to test my new NAMD. Only bond and angle are included in the psf file, the three atoms are aligned straight, each of them have a mass of 400 amu. But when I run the program, the simulation held still and had the following error.
BRACKET: 0 0 nan nan nan
After several try and visiting the Mailing list I found I was the Angle term tha caused the problem. When I turned it off or set the Ktheta zore the problem dissappeared. I already set a large enough boundry box the contain all the atoms within it. I know it might be a little inappropriate to use NAMD do to such a simple simulation, for it can cause various problems. But I really want to know how does it work and how to solve these problems. So please help, thank you.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:13 CST