Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD

From: Charline FAGNEN (charline.fagnen_at_upmc.fr)
Date: Tue Jan 09 2018 - 10:09:16 CST

Hello,

I am sorry for disrupting you, I have noticed the values of pressure
are strange : between 258 and -308 bar in my original molecular
dynamics and my restart. I have searched and asked to a friend but he
has the same thing, I have seen on NAMD standard output you have found
-616,05673 bar. Is it normal ? If yes, why do we have such big values ?

My second question concerns the Pressavg and Gpressavg, the first step
of my restart output has a very different value than my last value of
the previous molecular dynamics. I have read
« The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature
and pressure values since the previous ENERGY output; for the first
step in the simulation they will be identical to TEMP, PRESSURE, and
GPRESSURE. » so why the value is not the same as the last from the
previous molecular dynamics?

Thanks,

Sincerely,

Charline

Here is an extract of my input of restart :

# input
structure step5_assembly_final.xplor.psf
coordinates cluster1/namd_production1.1.restart.coor
velocities cluster1/namd_production1.1.restart.vel

#Continue a run
#binCoordinates cluster1/namd_production1.1.restart.coor
#binVelocities cluster1/namd_production1.1.restart.vel
extendedSystem cluster1/namd_production1.1.restart.xsc
firsttimestep 30500 # last step of previous run

paraTypeCharmm on;
margin 1.5

# output
set output cluster1/namd_production1.5ps
outputname ${output}
dcdfile cluster1/namd_production1.5ps.dcd
xstFile cluster1/namd_production1.5ps.xst

binaryoutput no
binaryrestart no

# These are specified by CHARMM
exclude scaled1-4
1-4scaling 1.0
switching on
vdwForceSwitching yes;

cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
pairlistdist 16.0;
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2;

# Integrator Parameters
timestep 2.0; # fs/step
rigidBonds all;
nonbondedFreq 1;
fullElectFrequency 1;

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

# PBC
#cellBasisVector1 114.566 0 0
#cellBasisVector2 0 114.566 0
#cellBasisVector3 0 0 128.572
#cellOrigin 0.000 0.000 0.000

# PME (for full-system periodic electrostatics)

PME yes;
PMEInterpOrder 6; # interpolation order (spline
order 6 in charmm)
PMEGridSizeX 120; # should be close to the cell size
PMEGridSizeY 120; # corresponds to the charmm input
fftx/y/z
PMEGridSizeZ 144;

# Constant Pressure Control (variable volume)
useGroupPressure yes; # use a hydrogen-group based
pseudo-molecular viral to calcualte pressure and
                                        # has less fluctuation, is
needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell no; # yes for anisotropic system
like membrane
useConstantRatio no; # keeps the ratio of the unit
cell in the x-y plane constant A=B

langevinPiston on; # Nose-Hoover Langevin piston
pressure control
langevinPistonTarget 1.0; # target pressure in bar 1atm =
1.01325bar
langevinPistonPeriod 50.0; # oscillation period in fs.
correspond to pgamma T=50fs=0.05ps
                                        # f=1/T=20.0(pgamma)
langevinPistonDecay 25.0; # oscillation decay time.
smaller value correspons to larger random
                                        # forces and increased
coupling to the Langevin temp bath.
                                        # Equall or smaller than piston period
langevinPistonTemp 300; # coupled to heat bath

# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps
(keep low)
langevinTemp 300; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens

# run
run 2500; # 2500 steps * 2fs = 5000fs=5ps
normalement traj de 5 frames

Here is my output of restart :

Charm++> Running on MPI version: 2.2
Charm++> level of thread support used: MPI_THREAD_FUNNELED (desired:
MPI_THREAD_FUNNELED)
Charm++> Running in SMP mode: numNodes 1024, 1 worker threads per process
Charm++> The comm. thread both sends and receives messages
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID:
v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
[0] isomalloc.c> Disabling isomalloc because isomalloc disabled by conv-mach
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 64 unique compute nodes (64-way SMP).
Info: NAMD 2.10 for BlueGeneQ-MPI-smp
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:
Info: Based on Charm++/Converse 60601 for mpi-bluegeneq-smp-xlc
Info: Built jeu. mars 19 11:21:07 CET 2015 by ssos683 on turing2
Info: Running on 1024 processors, 1024 nodes, 64 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0355503 s
Info: 30 MB of memory in use based on Kernel_GetMemorySize on BG/Q
Info: Configuration file is essai-5ps.inp
Info: Working in the current directory
/gpfs5r/workgpfs/rech/suu/rsuu003/3zrs-namd
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE cluster1/namd_production1.1.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 30500
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 114.31 0 0
Info: PERIODIC CELL BASIS 2 0 114.31 0
Info: PERIODIC CELL BASIS 3 0 0 128.284
Info: PERIODIC CELL CENTER 0 0 0
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: REMOVING LOAD FROM NODE 0
Info: REMOVING LOAD FROM NODE 1
Info: REMOVING PATCHES FROM PROCESSOR 0
Info: REMOVING PATCHES FROM PROCESSOR 1
Info: MIN ATOMS PER PATCH 40
Info: VELOCITY FILE cluster1/namd_production1.1.restart.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME cluster1/namd_production1.5ps.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 31000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME cluster1/namd_production1.5ps.xst
Info: XST FREQUENCY 500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME cluster1/namd_production1.5ps
Info: RESTART FILENAME cluster1/namd_production1.5ps.restart
Info: RESTART FREQUENCY 2000
Info: SWITCHING ACTIVE
Info: VDW FORCE SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 16
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 1.5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 20
Info: ENERGY OUTPUT STEPS 500
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 5000
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 BAR
Info: OSCILLATION PERIOD IS 50 FS
Info: DECAY TIME IS 25 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 8.79243e-06 8.79243e-06 8.79243e-06
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 6
Info: PME GRID DIMENSIONS 120 120 144
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.10_BlueGeneQ-MPI-smp.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.10_BlueGeneQ-MPI-smp.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
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-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1515424195
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB cluster1/namd_production1.1.restart.coor
Info: STRUCTURE FILE step5_assembly_final.xplor.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS toppar/par_all36_prot.prm
Info: PARAMETERS toppar/par_all36_na.prm
Info: PARAMETERS toppar/par_all36_carb.prm
Info: PARAMETERS toppar/par_all36_lipid.prm
Info: PARAMETERS toppar/par_all36_cgenff.prm
Info: PARAMETERS toppar/toppar_all36_prot_retinol.str
Info: PARAMETERS toppar/toppar_all36_na_rna_modified.str
Info: PARAMETERS toppar/toppar_all36_carb_glycopeptide.str
Info: PARAMETERS toppar/toppar_all36_prot_fluoro_alkanes.str
Info: PARAMETERS toppar/toppar_all36_prot_na_combined.str
Info: PARAMETERS toppar/toppar_all36_prot_heme.str
Info: PARAMETERS toppar/toppar_all36_lipid_bacterial.str
Info: PARAMETERS toppar/toppar_all36_lipid_miscellaneous.str
Info: PARAMETERS toppar/toppar_all36_lipid_cholesterol.str
Info: PARAMETERS toppar/toppar_all36_lipid_yeast.str
Info: PARAMETERS toppar/toppar_all36_lipid_sphingo.str
Info: PARAMETERS toppar/toppar_all36_lipid_inositol.str
Info: PARAMETERS toppar/toppar_all36_lipid_cardiolipin.str
Info: PARAMETERS toppar/toppar_all36_lipid_detergent.str
Info: PARAMETERS toppar/toppar_all36_lipid_lps.str
Info: PARAMETERS toppar/toppar_water_ions.str
Info: PARAMETERS toppar/toppar_dum_noble_gases.str
Info: PARAMETERS toppar/toppar_all36_na_nad_ppi.str
Info: PARAMETERS toppar/toppar_all36_lipid_prot.str
Info: PARAMETERS toppar/toppar_all36_carb_glycolipid.str
Info: PARAMETERS toppar/toppar_all36_carb_imlab.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: FIRST TIMESTEP 30500
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT

Warning: DUPLICATE ANGLE ENTRY FOR CG331-CG2D1-CG331
PREVIOUS VALUES k=55 theta0=119 k_ub=0 r_ub=0
    USING VALUES k=48 theta0=123.5 k_ub=0 r_ub=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CG2D1-CG321-CG321-CG2D1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.9 n=1 delta=180
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
   k=0.14 n=1 delta=180
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
   k=0.05 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CG331-CG2D1-CG331-HGA3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.16 n=3 delta=0
Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
   k=0.3 n=3 delta=0
Info: SUMMARY OF PARAMETERS:
Info: 1204 BONDS
Info: 3894 ANGLES
Info: 10382 DIHEDRAL
Info: 272 IMPROPER
Info: 6 CROSSTERM
Info: 397 VDW
Info: 23 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 36629 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Info: TIME FOR READING PSF FILE: 295.85
Info: TIME FOR READING PDB FILE: 5.79184
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 172501 ATOMS
Info: 135535 BONDS
Info: 153879 ANGLES
Info: 164855 DIHEDRALS
Info: 3554 IMPROPERS
Info: 1036 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 146035 RIGID BONDS
Info: 371468 DEGREES OF FREEDOM
Info: 63095 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 63095 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 1.04694e+06 amu
Info: TOTAL CHARGE = 2.7746e-05 e
Info: MASS DENSITY = 1.03716 g/cm^3
Info: ATOM DENSITY = 0.102909 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 309.448 s, 83.3945 MB of memory in use
Info: Startup phase 0 took 0.00185675 s, 83.3945 MB of memory in use
Info: ADDED 453393 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 2.05013 s, 119.168 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 11.7447
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.92477e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 5.29396e-23 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 3.38813e-21 AT 11.7447
Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 4.24069e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 8.47033e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.68425e-15 AT 11.9138
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.7447
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.37915e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.2326e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.34377e-15 AT 11.9138
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.03398e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.0328e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 8.07794e-27 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.47999e-16 AT 11.9138
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.0595333 s, 119.168 MB of memory in use
Info: Startup phase 3 took 0.00182524 s, 119.168 MB of memory in use
Info: Startup phase 4 took 0.00300071 s, 120.484 MB of memory in use
Info: Startup phase 5 took 0.0017243 s, 120.484 MB of memory in use
Info: PATCH GRID IS 11 (PERIODIC) BY 5 (PERIODIC) BY 6 (PERIODIC)
Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00526751 0.0177209 0.00357946
Info: LARGEST PATCH (154) HAS 593 ATOMS
Info: TORUS A SIZE 2 USING 0 1
Info: TORUS B SIZE 2 USING 0 1
Info: TORUS C SIZE 4 USING 0 1 2 3
Info: TORUS D SIZE 2 USING 0 1
Info: TORUS E SIZE 2 USING 0 1
Info: TORUS MINIMAL MESH SIZE IS 2 BY 2 BY 4 BY 2 BY 2
Info: Placed 79.3939% of base nodes on same physical node as patch
Info: Startup phase 6 took 6.23135 s, 156.383 MB of memory in use
Info: PME using 14 x 14 x 13 pencil grid for FFT and reciprocal sum.
Info: PME Z PENCIL LOCATIONS: 7 11 15 23 27 31 39 43 47 55 ...
Info: PME Y PENCIL LOCATIONS: 3 13 19 21 29 35 37 45 51 53 ...
Info: PME X PENCIL LOCATIONS: 1 5 9 17 25 30 33 41 46 49 ...
Info: Startup phase 7 took 13.0586 s, 156.383 MB of memory in use
Info: Startup phase 8 took 0.0357342 s, 156.383 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00287905 s, 156.383 MB of memory in use
Info: CREATING 11220 COMPUTE OBJECTS
Info: Startup phase 10 took 0.00914409 s, 156.383 MB of memory in use
Info: useSync: 1 useProxySync: 0
Info: Startup phase 11 took 0.00181798 s, 156.383 MB of memory in use
Info: Startup phase 12 took 0.000502433 s, 156.383 MB of memory in use
Info: Finished startup at 330.906 s, 156.383 MB of memory in use

TCL: Running for 2500 steps
ENERGY: 30500 8486.4232 36261.7329 29600.8639
706.7095 -485745.2455 19433.0140 0.0000
0.0000 110414.9295 -280841.5725 299.1554
-391256.5020 -280149.2370 299.1554 -46.3147
-45.6806 1676246.6488 -46.3147 -45.6806

OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 331.961
LDB: ============== END OF LOAD BALANCING =============== 331.962
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 331.969
LDB: ============= START OF LOAD BALANCING ============== 336.051
LDB: Largest compute 5236 load 1.331637 is 74.2% of average load 1.794467
LDB: Average compute 0.148684 is 8.3% of average load 1.794467
LDB: Partitioning computes with target load 0.297368
LDB: Increased migratable compute count from 9240 to 11979
LDB: Largest unpartitionable compute is 0.210863
LDB: ============== END OF LOAD BALANCING =============== 336.295
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 336.322
Info: Initial time: 1024 CPUs 0.0512552 s/step 0.296616 days/ns
156.383 MB memory
LDB: ============= START OF LOAD BALANCING ============== 337.325
LDB: ============== END OF LOAD BALANCING =============== 337.327
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 337.333
LDB: ============= START OF LOAD BALANCING ============== 341.313
LDB: Largest compute 1540 load 0.342216 is 19.3% of average load 1.769271
LDB: Average compute 0.112541 is 6.4% of average load 1.769271
LDB: TIME 341.558 LOAD: AVG 1.76927 MAX 3.77365 PROXIES: TOTAL 3630
MAXPE 11 MAXPATCH 11 None MEM: 156.383 MB
LDB: TIME 341.862 LOAD: AVG 1.76927 MAX 2.12312 PROXIES: TOTAL 7525
MAXPE 22 MAXPATCH 31 TorusLB MEM: 156.383 MB
LDB: ============== END OF LOAD BALANCING =============== 341.954
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 341.98
Info: Initial time: 1024 CPUs 0.0493682 s/step 0.285695 days/ns
156.383 MB memory
LDB: ============= START OF LOAD BALANCING ============== 345.005
LDB: Largest compute 541 load 0.421538 is 18.7% of average load 2.253652
LDB: Average compute 0.138863 is 6.2% of average load 2.253652
LDB: TIME 345.259 LOAD: AVG 2.25365 MAX 2.72614 PROXIES: TOTAL 3630
MAXPE 11 MAXPATCH 11 None MEM: 156.383 MB
LDB: TIME 345.307 LOAD: AVG 2.25365 MAX 2.72614 PROXIES: TOTAL 7525
MAXPE 22 MAXPATCH 31 RefineTorusLB MEM: 156.383 MB
LDB: TIME 345.615 LOAD: AVG 2.25365 MAX 2.46878 PROXIES: TOTAL 7714
MAXPE 22 MAXPATCH 33 RefineTorusLB MEM: 156.383 MB
LDB: ============== END OF LOAD BALANCING =============== 345.649
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 345.673
Info: Initial time: 1024 CPUs 0.0302003 s/step 0.17477 days/ns 156.383
MB memory
LDB: ============= START OF LOAD BALANCING ============== 348.722
LDB: Largest compute 4470 load 0.415263 is 18.7% of average load 2.223989
LDB: Average compute 0.136030 is 6.1% of average load 2.223989
LDB: TIME 348.978 LOAD: AVG 2.22399 MAX 2.55068 PROXIES: TOTAL 3630
MAXPE 11 MAXPATCH 11 None MEM: 156.383 MB
LDB: TIME 349.027 LOAD: AVG 2.22399 MAX 2.55068 PROXIES: TOTAL 7714
MAXPE 22 MAXPATCH 33 RefineTorusLB MEM: 156.383 MB
LDB: TIME 349.143 LOAD: AVG 2.22399 MAX 2.43593 PROXIES: TOTAL 7699
MAXPE 22 MAXPATCH 33 RefineTorusLB MEM: 156.383 MB
LDB: ============== END OF LOAD BALANCING =============== 349.174
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 349.199
Info: Benchmark time: 1024 CPUs 0.0304689 s/step 0.176325 days/ns
156.383 MB memory
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE cluster1/namd_production1.5ps.dcd AT
STEP 31000
The last position output (seq=31000) takes 0.095 seconds, 156.383 MB
of memory in use
Info: Benchmark time: 1024 CPUs 0.0311706 s/step 0.180385 days/ns
156.383 MB memory
ENERGY: 31000 8609.2690 36295.0227 29649.6980
706.3947 -486522.0606 19745.3199 0.0000
0.0000 109957.0966 -281559.2597 297.9149
-391516.3564 -280878.0325 299.1595 77.7385
75.0359 1674020.1717 1.9559 1.8758

Info: Benchmark time: 1024 CPUs 0.030236 s/step 0.174977 days/ns
156.383 MB memory
Info: Benchmark time: 1024 CPUs 0.0299911 s/step 0.17356 days/ns
156.383 MB memory
Info: Benchmark time: 1024 CPUs 0.0299547 s/step 0.173349 days/ns
156.383 MB memory
Info: Benchmark time: 1024 CPUs 0.0299747 s/step 0.173464 days/ns
156.383 MB memory
ENERGY: 31500 8389.3255 36044.6004 29583.8625
717.0753 -486441.4139 20010.6937 0.0000
0.0000 110465.7970 -281230.0596 299.2932
-391695.8565 -280552.6966 299.2036 167.9722
165.4216 1677619.8018 0.7364 0.7967

WRITING COORDINATES TO DCD FILE cluster1/namd_production1.5ps.dcd AT
STEP 31500
The last position output (seq=31500) takes 0.065 seconds, 156.383 MB
of memory in use
ENERGY: 32000 8444.0900 36006.4743 29612.3286
707.4543 -486062.8237 19272.2767 0.0000
0.0000 110421.5107 -281598.6891 299.1732
-392020.1999 -280902.2008 299.1543 -48.4062
-46.9931 1676838.8532 0.2396 0.2074

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 32000
WRITING COORDINATES TO DCD FILE cluster1/namd_production1.5ps.dcd AT
STEP 32000
WRITING COORDINATES TO RESTART FILE AT STEP 32000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=32000) takes 9.331 seconds, 156.383 MB
of memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 32000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=32000) takes 8.006 seconds, 156.383 MB
of memory in use
ENERGY: 32500 8466.6546 35803.5932 29589.4252
731.7796 -485259.5119 18730.7087 0.0000
0.0000 110264.2658 -281673.0849 298.7471
-391937.3506 -280973.5155 298.9233 -309.1885
-307.2058 1677995.9624 0.8321 0.8931

WRITING COORDINATES TO DCD FILE cluster1/namd_production1.5ps.dcd AT
STEP 32500
The last position output (seq=32500) takes 0.065 seconds, 156.383 MB
of memory in use
WRITING COORDINATES TO DCD FILE cluster1/namd_production1.5ps.dcd AT
STEP 33000
The last position output (seq=33000) takes 0.060 seconds, 156.383 MB
of memory in use
ENERGY: 33000 8465.7658 35871.1419 29608.3952
699.9376 -485596.9423 19366.7732 0.0000
0.0000 109967.0938 -281617.8349 297.9420
-391584.9286 -280931.7896 298.4923 31.8856
32.2687 1676504.4109 3.2890 3.2365

WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 33000
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 33000
CLOSING COORDINATE DCD FILE cluster1/namd_production1.5ps.dcd
The last position output (seq=-2) takes 9.178 seconds, 166.000 MB of
memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 33000
The last velocity output (seq=-2) takes 7.950 seconds, 156.383 MB of
memory in use
====================================================

WallClock: 447.108765 CPUTime: 447.108765 Memory: 156.382812 MB
[Partition 0][Node 0] End of program

Charline Fagnen
PhD Student at IMPMC (UPMC) / ENS Paris Saclay
Mail: charline.fagnen_at_upmc.fr

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