Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 32 threads
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Nov-07-136676
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (64-way SMP).
Charm++> cpu topology info is gathered in 0.006 seconds.
Info: NAMD 2.12 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Running on 32 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0555959 s
CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue
Info: 2334.93 MB of memory in use based on /proc/self/stat
Info: Configuration file is run.conf
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: switchdist (switching)
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 110 0 0
Info: PERIODIC CELL BASIS 2 0 107.7 0
Info: PERIODIC CELL BASIS 3 0 0 91
Info: PERIODIC CELL CENTER 55.74 54.54 46.12
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 0.833333
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME ./outputs/t1y2020.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME ./outputs/t1y2020.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME ./outputs/t1y2020
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ./outputs/t1y2020.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 10
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 2
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 18
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 112 108 96
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.12_Linux-x86_64-multicore.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.12_Linux-x86_64-multicore.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-05
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1589474687
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./t1y_water.prmtop
Info: AMBER COORDINATE FILE ./t1y_water.inpcrd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (./t1y_water.prmtop) ...
PARM file in AMBER 7 format Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS. Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY. Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY. Warning: Encounter 10-12 H-bond term Warning: Found 28843 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 44 BONDS
Info: 92 ANGLES
Info: 92 HARMONIC
Info: 0 COSINE-BASED
Info: 48 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 153 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PDB FILE: 1.69277e-05
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 95737 ATOMS
Info: 95829 BONDS
Info: 16841 ANGLES
Info: 35533 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 136921 EXCLUSIONS
Info: 91126 RIGID BONDS
Info: 196085 DEGREES OF FREEDOM
Info: 33454 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 33454 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 585252 amu
Info: TOTAL CHARGE = -1.68988e-06 e
Info: MASS DENSITY = 0.901472 g/cm^3
Info: ATOM DENSITY = 0.0888035 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 8.21327 s, 2471.26 MB of memory in use
Info: Startup phase 0 took 0.000333071 s, 2471.26 MB of memory in use
Info: ADDED 0 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0468209 s, 2482.88 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290479 AT 0.251946
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000178193 AT 9.97184
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.00974e-28 AT 9.99687
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 6.2204e-22 AT 9.99687
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00110817 s, 2482.88 MB of memory in use
Info: Startup phase 3 took 0.000199795 s, 2482.88 MB of memory in use
Info: Startup phase 4 took 0.00692105 s, 2482.88 MB of memory in use
Info: Startup phase 5 took 0.000262022 s, 2482.88 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00743926 0.0386896 -0.0070714
Info: LARGEST PATCH (68) HAS 716 ATOMS
Info: TORUS A SIZE 32 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0348861 s, 2499.81 MB of memory in use
Info: PME using 28 and 27 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 11 ...
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Startup phase 7 took 0.00529599 s, 2499.81 MB of memory in use
Info: Startup phase 8 took 0.00334787 s, 2499.81 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00493598 s, 2499.81 MB of memory in use
Info: CREATING 3160 COMPUTE OBJECTS
Info: useSync: 0 useProxySync: 0
Info: Startup phase 10 took 0.056572 s, 2499.81 MB of memory in use
Info: Startup phase 11 took 0.000294209 s, 2499.81 MB of memory in use
Info: Startup phase 12 took 0.000485897 s, 2499.81 MB of memory in use
Info: Finished startup at 8.37473 s, 2499.81 MB of memory in use
TCL: Minimizing for 30000 steps Warning: Bad global bond count! (95828 vs 95829) Warning: Bad global angle count! (16837 vs 16841) Warning: Bad global dihedral count! (35510 vs 35533) Warning: Low global exclusion count! (136877 vs 136921) Warning: This warning is not unusual during minimization. Warning: Increasing pairlistdist or cutoff may avoid this.
PRESSURE: 0 9.37973e+10 4.06414e+10 1.31199e+11 4.06414e+10 1.76223e+10 5.6857e+10 1.31199e+11 5.6857e+10 1.83529e+11
GPRESSURE: 0 -7.21723e+11 9.71225e+10 6.12946e+11 -3.12813e+11 4.21002e+10 2.6565e+11 -1.00962e+12 1.35868e+11 8.5744e+11
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 69 ATOMS WITH BAD CONTACTS DOWNHILL
Warning: Bad global bond count! (95828 vs 95829)
Warning: Bad global angle count! (16837 vs 16841)
Warning: Bad global dihedral count! (35510 vs 35533)
Warning: Low global exclusion count! (136877 vs 136921)
Warning: This warning is not unusual during minimization.
Warning: Increasing pairlistdist or cutoff may avoid this.
PRESSURE: 1 6.41534e+09 6.67329e+09 2.45262e+10 6.67329e+09 6.94536e+09 2.55174e+10 2.45262e+10 2.55174e+10 9.37826e+10
GPRESSURE: 1 -7.12037e+10 1.20488e+10 7.03779e+10 -7.40848e+10 1.25376e+10 7.32207e+10 -2.72266e+11 4.60726e+10 2.69106e+11
ENERGY: 1 178329.3651 2218.5431 5963.1686 0.0000 -298941.8018 9999999999.9999 0.0000 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 1078077.0000 9999999999.9999 9999999999.9999
作者Author: ene 时间: 2020-5-17 02:07
你对接出来的结构有问题吧，感觉是原子可能有重叠的地方，一般Bad global xxx count这类报错是这种原因，另外vDW能量都飞了……