From: ershela.durresi_at_yale.edu
Date: Tue Jun 09 2009 - 05:58:20 CDT
Dear all,
I am trying to run a simulation on NAMD and the simulation aborts almost
immediately after I try to run it. In the output file I notice that the
simulation parameter data keeps repeating (below is the part that keeps
repeating), which has not happened to me before. I tried to run another
simulation of a similar size (only 40 atoms larger), and in that case I got the
simulation to run. I would be extremely grateful if you could please offer any
advice.
Thank you so much,
Ershela
Info: Running on 1 processors.
Info: 1333 kB of memory in use.
Info: Running on 1 processors.
Info: 1333 kB of memory in use.
Measuring processor speeds... Done.
TCL: Suspending until startup complete.
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Measuring processor speeds... Done.
TCL: Suspending until startup complete.
Info: Changed directory to .
Info: Configuration file is Actin_ADF_run.namd
Info: Changed directory to .
Info: Configuration file is Actin_ADF_run.namd
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 5000000
Info: STEPS PER CYCLE 16
Info: PERIODIC CELL BASIS 1 113 0 0
Info: PERIODIC CELL BASIS 2 0 115 0
Info: PERIODIC CELL BASIS 3 0 0 111
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 3200 steps
Info: FIRST LDB TIMESTEP 80
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: VELOCITY FILE equil_out_T300.vel
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME 5000ps.dcd
Info: DCD FREQUENCY 20000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME 5000ps.xst
Info: XST FREQUENCY 20000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME 5000ps
Info: RESTART FILENAME ./res
Info: RESTART FREQUENCY 100000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 12
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 10
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 24.5
Info: ENERGY OUTPUT STEPS 10000
Info: MOMENTUM OUTPUT STEPS 10000
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 10000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
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 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 310 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 113 116 112
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 5000000
Info: STEPS PER CYCLE 16
Info: PERIODIC CELL BASIS 1 113 0 0
Info: PERIODIC CELL BASIS 2 0 115 0
Info: PERIODIC CELL BASIS 3 0 0 111
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 3200 steps
Info: FIRST LDB TIMESTEP 80
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: VELOCITY FILE equil_out_T300.vel
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 5000000
Info: STEPS PER CYCLE 16
TCL: Suspending until startup complete.
Info: DCD FILENAME 5000ps.dcd
Info: DCD FREQUENCY 20000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME 5000ps.xst
Info: XST FREQUENCY 20000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME 5000ps
Info: PERIODIC CELL BASIS 1 113 0 0
Info: PERIODIC CELL BASIS 2 0 115 0
Info: PERIODIC CELL BASIS 3 0 0 111
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 3200 steps
Info: FIRST LDB TIMESTEP 80
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: RESTART FILENAME ./res
Info: RESTART FREQUENCY 100000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: BINARY RESTART FILES WILL BE USED
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: VELOCITY FILE equil_out_T300.vel
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 12
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME 5000ps.dcd
Info: DCD FREQUENCY 20000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: PAIRLISTS ENABLED
Info: MARGIN 10
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 24.5
TCL: Suspending until startup complete.
Info: XST FILENAME 5000ps.xst
Info: XST FREQUENCY 20000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME 5000ps
Info: ENERGY OUTPUT STEPS 10000
Info: MOMENTUM OUTPUT STEPS 10000
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 10000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
TCL: Suspending until startup complete.
Info: RESTART FILENAME ./res
Info: RESTART FREQUENCY 100000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: BINARY RESTART FILES WILL BE USED
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Charm++: standalone mode (not using charmrun)
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 113 116 112
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 12
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Info: PAIRLISTS ENABLED
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 5000000
Info: STEPS PER CYCLE 16
Info: MARGIN 10
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 24.5
Info: ENERGY OUTPUT STEPS 10000
Info: MOMENTUM OUTPUT STEPS 10000
Info: TIMING OUTPUT STEPS 10000
Info: PERIODIC CELL BASIS 1 113 0 0
Info: PERIODIC CELL BASIS 2 0 115 0
Info: PERIODIC CELL BASIS 3 0 0 111
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 3200 steps
Info: FIRST LDB TIMESTEP 80
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: PRESSURE OUTPUT STEPS 10000
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: VELOCITY FILE equil_out_T300.vel
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: DCD FILENAME 5000ps.dcd
Info: DCD FREQUENCY 20000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME 5000ps.xst
Info: XST FREQUENCY 20000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME 5000ps
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: RESTART FILENAME ./res
Info: RESTART FREQUENCY 100000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 12
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
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 113 116 112
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: PAIRLISTS ENABLED
Info: MARGIN 10
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 24.5
Info: ENERGY OUTPUT STEPS 10000
Info: MOMENTUM OUTPUT STEPS 10000
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 10000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: NAMD 2.5 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.5 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Info: 1 NAMD 2.5 Linux-i686 1 ib072.bulldogj pd234
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Charm++: standalone mode (not using charmrun)
Info: Running on 1 processors.
Info: 1333 kB of memory in use.
Info: 1 NAMD 2.5 Linux-i686 1 ib074.bulldogj pd234
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 113 116 112
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Measuring processor speeds... Done.
Info: Running on 1 processors.
Info: 1333 kB of memory in use.
Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
Info: Changed directory to .
Measuring processor speeds... Done.
Info: NAMD 2.5 for Linux-i686
Info:
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