From: sciencekey (sciencekey_at_163.com)
Date: Tue Apr 05 2011 - 04:00:11 CDT
Hi, everyone,
I am a starter of NAMD. Recently, I download the latest version of NAMD and namd-tutorial-file. According to the tutorial, I get all the necessary file. But at last, when I run namd, the program only generated the ubq_ws_eq.log file. In oder to find out the questions, I used the original file ubq.pdb, ubq.psf, ubq_ws.pdb and ubq_ws.pdf from the namd-tutorial-file package and then carry out the program namd2 again. But the question still appeared. Only the log file appeared and namd2 cannot generate other file such as ubq_ws_eq.dcd, ubq_ws_eq.coor, etc. Could anybody help me?
My operation system: windows7 home premium; processor: intel core i5 CPU; Type: 64-bit operation system
The verison of NAMD: I tried two versions, NAMD_2.8b1_Win32-multicore and NAMD_2.7_Win32. They all have the same result. the version NAMD_2.8b1_Win64-MPI didn't work in my system.
The brief content of log file:
.............................................
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-021 AT 11.8295
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-014 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-022 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138
Info: Startup phase 8 took 0.00300002 s, 8.43359 MB of memory in use
Info: Startup phase 9 took 0.000999928 s, 12.2305 MB of memory in use
Info: Finished startup at 0.188 s, 12.2305 MB of memory in use
TCL: Minimizing for 100 steps
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
ENERGY: 0 1947.9207 1238.5705 263.8635 10.7301 -18781.7697 1984.0072 9999999999.9999 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000
MINIMIZER SLOWLY MOVING 3430 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 0 0 0 0 0 0 0 0 0
GPRESSURE: 1 0 0 0 0 0 0 0 0 0
ENERGY: 1 3223.1201 1535.3414 276.6121 37.1532 -18789.9225 2068.2274 9999999999.9999 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000
.........................
LDB: ============= START OF LOAD BALANCING ============== 10.322
LDB: ============== END OF LOAD BALANCING =============== 10.322
LDB: =============== DONE WITH MIGRATION ================ 10.322
MINIMIZER SLOWLY MOVING 3719 ATOMS WITH BAD CONTACTS DOWNHILL
Warning: Low global exclusion count, possible error!
Warning: This warning is not unusual during minimization.
Warning: Increasing pairlistdist or cutoff may avoid this.
PRESSURE: 100 0 0 0 0 0 0 0 0 0
GPRESSURE: 100 0 0 0 0 0 0 0 0 0
Info: Initial time: 1 CPUs 0.10126 s/step 0.585995 days/ns 21.0977 MB memory
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
ENERGY: 100 3392324.1635 199515.7535 1811.2055 13105.3786 -8263.5514 9999999999.9999 9999999999.9999 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 308!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 291!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 993!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atom 539 velocity is 1.73587e+249 31.2351 158.784 (limit is 6000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 927!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 327!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 720!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 39!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 490!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atom 112 velocity is 289.834 -8.79866e+015 1.17204e+225 (limit is 6000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 94!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1187!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 755!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 666!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 612!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 137!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1227!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================
WallClock: 10.892000 CPUTime: 10.891000 Memory: 21.203125 MB
Program finished.
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