Trouble in energy minimization with warning to increase cutoff

From: Eva Nong (nong2_at_fas.harvard.edu)
Date: Tue Jun 17 2008 - 18:57:49 CDT

Hi,

I generated a PSF file following the NAMD tutorial and solvated and ionized a system just fine. But when I tried to run the first minimization I got the warning

Warning: Bad global exclusion count, possible error!

Warning: Increasing cutoff during minimization may avoid this.

I have the following periodic boundary conditions for the 33188-atom system:

cellBasisVector1 70 0. 0.

cellBasisVector2 0. 80 0.

cellBasisVector3 0. 0. 70

cellOrigin -6.01714372635 37.4773597717 -7.95362949371 (generated from VMD measurecenter)

I tried changing the cutoff and pairlist to 20+ from ~12 angstroms but it didn't help. Could you help me out?

my files can be located at:

http://www.hcs.harvard.edu/~prisemag/eva/files/min3ktq.pme

http://www.hcs.harvard.edu/~prisemag/eva/files/min3ktq.out

http://www.hcs.harvard.edu/~prisemag/eva/files/solvate3ktq.psf

Thank you!

Eva

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