From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Feb 18 2015 - 18:59:28 CST
That error means that your system is unstable. It could be a problem
with your model. You may want to try using a smaller timestep, e.g.
10-25 fs.
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Wed, Feb 18, 2015 at 6:29 PM, Yongcheng Zhou
<yzhou_at_math.colostate.edu> wrote:
>
> Dear all, I was tring to do a sterred residue-based coarse grained
> simulation of a very small protein 1AJJ, but got the following error
> before the the first step of the simulation:
>
> FATAL ERROR: Low global exclusion count! System unstable or
> pairlistdist or cutoff too small
>
> There actually is a thread in this maillist on a similar problem years ago:
>
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/3805.html
>
> but no final solution was given unfortunately. I am attaching the pdb, psf,
> and ref files here, and the info below produced following this
> suggestion
>
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/3814.html
>
> might be helpful too if anyone would want to help with this.
>
>
> Many thanks!
>
> Yongcheng
>
> -------------------------------------------------------------------------
> cellBasisVector1 19.894999235868454 0 0
> cellBasisVector2 0 21.364999771118164 0
> cellBasisVector3 0 0 26.67400074005127
> cellOrigin 11.019709587097168 6.169844150543213 3.2374091148376465
> Particle count: 83
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