Re: Trouble in energy minimization with warning to increase cutoff

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 18 2008 - 00:01:29 CDT

The most frequent cause for this is an unrealistically long distance
between bonded atoms in your system. The first step is to verify that
your chains were split properly, and inspect your system (in vmd, with
the psf and pdb loaded) to see if any bonds are present between distant
atoms.
Best,
Peter

Eva Nong wrote:
> 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/%7Eprisemag/eva/files/min3ktq.pme>
>
> http://www.hcs.harvard.edu/~prisemag/eva/files/min3ktq.out
> <http://www.hcs.harvard.edu/%7Eprisemag/eva/files/min3ktq.out>
>
> http://www.hcs.harvard.edu/~prisemag/eva/files/solvate3ktq.psf
> <http://www.hcs.harvard.edu/%7Eprisemag/eva/files/solvate3ktq.psf>
>
> Thank you!
>
> Eva
>
>
>
>
>
>
>

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