RE: Gradient tolerance nan for A three-atom simulation

From: accomp lin (
Date: Tue Jan 06 2009 - 22:20:18 CST

Hi Gumbart

Thanks very much for your help.The problem had been solved when I altered the angle a little from 180.(My theta0 is also 180 degree).
However , I got another error , it said:

Reason: FATAL ERROR: Bad global exclusion count!

The problem occurs at different time step with different set of initial coordinates of the atoms. I then I changed the cutoff , switchdist, and  pairlistdist to be very little and set the parameter of LJ potential zore, the simulation ran successfully. But when I set the cutoff, swithdist and pairlistdist to be normal, the error came back again. Wht does these parameter matter, since the LJ potential is already zore? How come it to be a problem in my three-atoms system?

Thanks, best.


--- 09年1月6日,周二, JC Gumbart <> 写道:
发件人: JC Gumbart <>
主题: RE: namd-l: Gradient tolerance nan for A three-atom simulation
日期: 2009,16,周二,1:24下午


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

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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