From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 29 2011 - 11:50:00 CDT
Dear Massimiliano,
It's unclear if you're coarse-grain sim is a residue-based or shape-based
coarse-grain model.
Have you tried restarting the sim, and does it repeat the error or continue
successfully?
Have you loaded the last few frames corresponding to the last few steps of
the sim to insure you aren't experience some non-physical behavior or
particles with high velocities?
Best,
Chris
On Mon, Aug 29, 2011 at 9:36 AM, Massimiliano Porrini <M.Porrini_at_ed.ac.uk>wrote:
> Dear namd-lers,
>
> I am attempting to perform some coarse grained (CG) MD simulations.
> After having successfully coarse-grained my system with the VMD utility
> and minimised the structure with namd, I tried to equilibrate the
> temperature
> at 320 K, but I get the following error soon at the beginning of the run:
>
> FATAL ERROR: Low global exclusion count! System unstable or
> pairlistdist or cutoff too small.
>
> I tried to increased either the cut-off or the PairListDist or both but
> with no success.
>
> Any hint to overcome this problem would be really appreciated.
>
> All the best,
> MP
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini_at_ed.ac.uk
> mozz76_at_gmail.com
> maxp_at_iesl.forth.gr
>
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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