Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small.

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Mon Aug 29 2011 - 14:26:06 CDT

Dear Chris,

Apologies for not being clearer, the model I adopted is the residue-based one.

I can not apply either of the two solutions you suggested because the
simulation stops before running, I mean the error occur upon the beginning,
and no snapshot is produced, as you can see from the output excerpt below:

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
REINITIALIZING VELOCITIES AT STEP 0 TO 0 KELVIN.
TCL: Running for 20 steps
FATAL ERROR: Low global exclusion count! System unstable or
pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Low global exclusion count! System unstable or
pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Charm++ fatal error:
FATAL ERROR: Low global exclusion count! System unstable or
pairlistdist or cutoff too small.

FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

[0] Stack Traceback:
  [0:0] CmiAbort+0x93 [0xbed6fb]
  [0:1] _Z8NAMD_bugPKc+0x85 [0x5328e3]
  [0:2] _ZN10Controller16compareChecksumsEii+0x547 [0x866d79]
  [0:3] _ZN10Controller21printDynamicsEnergiesEi+0x17 [0x871165]
  [0:4] _ZN10Controller9integrateEv+0x134 [0x86aa84]
  [0:5] _ZN10Controller9algorithmEv+0x5dc [0x85d936]
  [0:6] _ZN10Controller9threadRunEPS_+0xe [0x8726f8]
  [0:7] CthStartThread+0x29 [0xb16461]
  [0:8] +0x44cb0 [0x7f315763dcb0]
[0] Stack Traceback:
  [0:0] [0xbee6dd]
  [0:1] CmiAbort+0xd1 [0xbed739]
  [0:2] _Z8NAMD_bugPKc+0x85 [0x5328e3]
  [0:3] _ZN10Controller16compareChecksumsEii+0x547 [0x866d79]
  [0:4] _ZN10Controller21printDynamicsEnergiesEi+0x17 [0x871165]
  [0:5] _ZN10Controller9integrateEv+0x134 [0x86aa84]
  [0:6] _ZN10Controller9algorithmEv+0x5dc [0x85d936]
  [0:7] _ZN10Controller9threadRunEPS_+0xe [0x8726f8]
  [0:8] CthStartThread+0x29 [0xb16461]
  [0:9] +0x44cb0 [0x7f315763dcb0]
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

Besides I visualized the last frame of the minimization and it "seems OK".

All the best,
MP

2011/8/29 Chris Harrison <charris5_at_gmail.com>:
> 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
>
>

-- 
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

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