From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 29 2011 - 19:35:42 CDT
Dear Massimiliano,
Can you send me your log file and config file, maybe off-list?
Could you also load your system in vmd, entire the below text into the tkcon
and send me the output? Make sure your system is the top molecule in VMD.
proc get_cell {{molid top}} {
set all [atomselect $molid all]
set minmax [measure minmax $all]
set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]
puts "cellBasisVector1 [lindex $vec 0] 0 0"
puts "cellBasisVector2 0 [lindex $vec 1] 0"
puts "cellBasisVector3 0 0 [lindex $vec 2]"
set center [measure center $all]
puts "cellOrigin $center"
puts "Particle count: [$all num]"
$all delete
}
get_cell
Best,
Chris
-- 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 Massimiliano Porrini <M.Porrini_at_ed.ac.uk> writes: > Date: Mon, 29 Aug 2011 20:26:06 +0100 > From: Massimiliano Porrini <M.Porrini_at_ed.ac.uk> > To: Chris Harrison <charris5_at_gmail.com> > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: FATAL ERROR: Low global exclusion count! System > unstable or pairlistdist or cutoff too small. > > 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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