RE: Gradient tolerance nan for A three-atom simulation

From: JC Gumbart (
Date: Mon Jan 05 2009 - 23:24:35 CST

I wonder if this happens because theta=180 is an indeterminate problem? What if you try offsetting the third atom from the line of the other two? What is the theta0 you’ve set in the parameter file?



From: [] On Behalf Of accomp lin
Sent: Monday, January 05, 2009 11:10 PM
Subject: namd-l: Gradient tolerance nan for A three-atom simulation


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.



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