From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Sat May 07 2016 - 07:45:54 CDT
Please minimise the system for more duration., it seems that your system is not enough minimised
On 7 May 2016, at 7:17 PM, Srijita Paul <srijitap91_at_gmail.com> wrote:
Hii
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 10000
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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