H:\eqtii-i18c_fbnp_2ft_2ft_4ft>echo calculating MD 1>C:\Resident\busy.txt Charm++: standalone mode (not using charmrun) CmiMemory: fences and atomic operations not available in native assembly [0] isomalloc.c> Disabling isomalloc because mmap() does not work Charm++> cpu topology info is being gathered. Charm++> Running on 1 unique compute nodes (8-way SMP). Info: NAMD 2.7b2 for Win32 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu Info: Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 60103 for multicore-win32 Info: Built Thu Nov 12 22:32:06 CST 2009 by jcphill on honor Info: Running on 8 processors. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.109 s Info: 4.85156 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is eqtii-i18c_20ns.1.restart.conf TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE out/eqtii-i18c_20ns.1.c.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 5853380 Info: STEPS PER CYCLE 20 Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB 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: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE out/eqtii-i18c_20ns.1.c.restart.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 74.2 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME out/eqtii-i18c_20ns.1.d.dcd Info: DCD FREQUENCY 207 Info: DCD FIRST STEP 5853587 Info: XST FILENAME out/eqtii-i18c_20ns.1.d.xst Info: XST FREQUENCY 207 Info: VELOCITY DCD FILENAME out/eqtii-i18c_20ns.1.d.dcd.vel Info: VELOCITY DCD FREQUENCY 207 Info: VELOCITY DCD FIRST STEP 5853587 Info: OUTPUT FILENAME out/eqtii-i18c_20ns.1.d Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME out/eqtii-i18c_20ns.1.d.restart Info: RESTART FREQUENCY 207 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 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: PAIRLIST OUTPUT STEPS 207 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16 Info: ENERGY OUTPUT STEPS 207 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 207 Info: PRESSURE OUTPUT STEPS 207 Info: FIXED ATOMS ACTIVE Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C2 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: RIGID BONDS TO HYDROGEN : ALL Info: ERROR TOLERANCE : 1e-008 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1277283355 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB eqtii-i18c.pdb Info: STRUCTURE FILE eqtii-i18c.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipid_pf.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES out/eqtii-i18c_20ns.1.c.restart.coor Info: FIRST TIMESTEP 5853380 Info: SUMMARY OF PARAMETERS: Info: 188 BONDS Info: 462 ANGLES Info: 559 DIHEDRAL Info: 51 IMPROPER Info: 0 CROSSTERM Info: 93 VDW Info: 0 VDW_PAIRS Info: TIME FOR READING PSF FILE: 0.156 Info: TIME FOR READING PDB FILE: 0 Info: Info: Reading from binary file out/eqtii-i18c_20ns.1.c.restart.coor Info: **************************** Info: STRUCTURE SUMMARY: Info: 2810 ATOMS Info: 2846 BONDS Info: 5117 ANGLES Info: 7494 DIHEDRALS Info: 460 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 717 FIXED ATOMS Info: 1396 RIGID BONDS Info: 0 RIGID BONDS BETWEEN FIXED ATOMS Info: 4883 DEGREES OF FREEDOM Info: 1414 HYDROGEN GROUPS Info: 364 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 20018.9 amu Info: TOTAL CHARGE = 11 e Info: ***************************** Info: Info: Entering startup at 0.313 s, 11.4961 MB of memory in use Info: Startup phase 0 took 0 s, 11.4961 MB of memory in use Info: Startup phase 1 took 0.0309999 s, 12.1914 MB of memory in use Info: Startup phase 2 took 0 s, 12.3398 MB of memory in use Info: PATCH GRID IS 3 BY 3 BY 2 Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file out/eqtii-i18c_20ns.1.c.restart.vel Info: REMOVING COM VELOCITY 0.105949 -0.0153836 0.0912875 Info: LARGEST PATCH (13) HAS 432 ATOMS Info: CREATING 241 COMPUTE OBJECTS Info: Startup phase 3 took 0 s, 13.0313 MB of memory in use Info: Startup phase 4 took 0 s, 13.0313 MB of memory in use Info: Startup phase 5 took 0 s, 13.043 MB of memory in use LDB: Measuring processor speeds ... Done. Info: Startup phase 6 took 1.234 s, 13.043 MB of memory in use Info: CREATING 241 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS 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 7 took 0.0309999 s, 14.1172 MB of memory in use Info: Startup phase 8 took 0 s, 16.6172 MB of memory in use Info: Finished startup at 1.609 s, 16.6172 MB of memory in use TCL: Running for 4146620 steps Info: Pairlistdist is too small for 1 computes during timestep 5853387. LDB: ============= START OF LOAD BALANCING ============== 3.047 LDB: ============== END OF LOAD BALANCING =============== 3.047 Info: Initial time: 8 CPUs 0.01437 s/step 0.0831597 days/ns 21.9063 MB memory PRESSURE: 5853546 0 0 0 0 0 0 0 0 0 GPRESSURE: 5853546 0 0 0 0 0 0 0 0 0 PRESSAVG: 5853546 0 0 0 0 0 0 0 0 0 GPRESSAVG: 5853546 0 0 0 0 0 0 0 0 0 Info: 18 pairlist warnings in past 207 steps. ENERGY: 5853546 253.6481 1212.7151 808.4749 40.5836 -179.1909 -311.7182 0.0000 0.0000 1435.7173 3260.2299 295.9188 1824.5126 3279.9014 307.6724 OPENING EXTENDED SYSTEM TRAJECTORY FILE WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5853546 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 5853546 WRITING COORDINATES TO RESTART FILE AT STEP 5853546 FINISHED WRITING RESTART COORDINATES OPENING VELOCITY DCD FILE WRITING VELOCITIES TO DCD FILE AT STEP 5853546 WRITING VELOCITIES TO RESTART FILE AT STEP 5853546 FINISHED WRITING RESTART VELOCITIES Info: Pairlistdist is too small for 1 computes during timestep 5853549. LDB: ============= START OF LOAD BALANCING ============== 4.469 LDB: TIME 4.484 LOAD: AVG 0.619874 MAX 1.438 PROXIES: TOTAL 34 MAXPE 7 MAXPATCH 4 None 0.102 LDB: TIME 4.484 LOAD: AVG 0.619874 MAX 0.736999 PROXIES: TOTAL 48 MAXPE 10 MAXPATCH 5 TorusLB 0.102 LDB: TIME 4.484 LOAD: AVG 0.619874 MAX 0.645999 PROXIES: TOTAL 48 MAXPE 10 MAXPATCH 5 TorusLB 0.102 LDB: ============== END OF LOAD BALANCING =============== 4.5 H:\eqtii-i18c_fbnp_2ft_2ft_4ft>del C:\Resident\busy.txt