From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Sun May 08 2016 - 20:19:44 CDT
If you don't get reasonable energies after 10000 steps of minimization,
there is something wrong with how your system is constructed. Possible
problems can be a poorly chosen initial size or major clashes in the
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Sat, May 7, 2016 at 6:17 AM, Srijita Paul <srijitap91_at_gmail.com> wrote:
> I am facing a problem during minimisation and heating.The job is
> automatically being stopped after few steps showing such type of error-
> LINE MINIMIZER BRACKET: DX 0 inf DU -nan -nan DUDX nan nan nan
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> Warning: Low global exclusion count! (92292 vs 92346)
> Warning: This warning is not unusual during minimization.
> Warning: Increasing pairlistdist or cutoff may avoid this.
> PRESSURE: 10000 -nan nan nan nan -nan nan nan nan -nan
> GPRESSURE: 10000 nan nan nan nan nan nan nan nan nan
> TIMING: 10000 CPU: 32969.1, 3.29687/step Wall: 32959, 3.29586/step, 0
> hours remaining, 1132.691406 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 10000 9999999999.9999 9999999999.9999 9999999999.9999
> 9999999999.9999 9999999999.9999 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 0.0000 9999999999.9999 9999999999.9999
> 1061208.0000 9999999999.9999 9999999999.9999
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
> WRITING COORDINATES TO DCD FILE protein_choline_urea_wat_nvt.dcd AT STEP
> WRITING COORDINATES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART COORDINATES
> The last position output (seq=10000) takes 0.002 seconds, 1132.691 MB of
> memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART VELOCITIES
> REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN.
> TCL: Running for 10000 steps
> FATAL ERROR: Low global exclusion count! (92292 vs 92346) System
> unstable or pairlistdist or cutoff too small.
> In my configuration file cutoff is 12 and pairlistdist is 14.
> My system contains protein urea choline-o-sulfate and water.total there is
> 50712 atoms.Box volume 100*100*100.
> please give me some guidance about it.
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