From: linefinc (linefinc_at_gmail.com)
Date: Mon Jun 19 2006 - 11:50:41 CDT
I work as usual on my CO2 molecule bat i don't find the problem in my
simulation.
I have made too mach experiment bat i don't resolve the problem.
I wont made a CO2 solvent box, it is cubic and with 36A of side. In
this box there's 300 molecules.
I use packmol to generate it. To avoid problem with periodic boundary
conditions i generate a box 4A smaller.
The box start in {2.0 2.0 2.0} and end at {34.0 34.0 34.0}, the
tolerance is 4.5A between any molecule.
I generate correctly the psf. On this solvent box, I measure bounding
box that correspond with the input data of packmol.
>Main< (Desktop) 51 % measure minmax [atomselect top all]
{2.0 2.0 2.0} {34.0 34.0 34.0}
now i run the simulation on windows and namd plot out (below).
I run the simulation on linux end plot a different error!
Possible !?!?!?
I don't understend where is located the error.
TNX
Sassaro
############### WINDOWS ###############
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6b1 for Win32-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 50900 for net-win32-smp
Info: Built Fri Jul 29 12:33:47 2005 by administrator on malta
Info: Running on 1 processors.
Info: 0 kB of memory in use.
Info: Changed directory to C:\Documents and Settings\Matteo\Desktop\co2
Info: Configuration file is min_solv.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 36 0 0
Info: PERIODIC CELL BASIS 2 0 36 0
Info: PERIODIC CELL BASIS 3 0 0 36
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM 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: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME sim_out.dcd
Info: DCD FREQUENCY 10
Info: DCD FIRST STEP 10
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME sim_out
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14.5
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 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 17
Info: ENERGY OUTPUT STEPS 1000
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1150733412
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB mixture.pdb
Info: STRUCTURE FILE mixture.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 1 BONDS
Info: 1 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 2 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 900 ATOMS
Info: 600 BONDS
Info: 300 ANGLES
Info: 0 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 EXCLUSIONS
Info: 2697 DEGREES OF FREEDOM
Info: 900 HYDROGEN GROUPS
Info: TOTAL MASS = 13202.7 amu
Info: TOTAL CHARGE = 0 e
Info: *****************************
Info: Entering startup phase 0 with 0 kB of memory in use.
Info: Entering startup phase 1 with 0 kB of memory in use.
Info: Entering startup phase 2 with 0 kB of memory in use.
Info: Entering startup phase 3 with 0 kB of memory in use.
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0452495 -0.157624 -0.0325843
Info: LARGEST PATCH (6) HAS 117 ATOMS
Info: Entering startup phase 4 with 0 kB of memory in use.
Info: Entering startup phase 5 with 0 kB of memory in use.
Info: Entering startup phase 6 with 0 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 0 kB 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-021 AT 11.8295
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-014 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 9.09495e-013 AT 0.03125
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.75 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 19968 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 6.16499e-015 AT 0.0441942
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: Entering startup phase 8 with 0 kB of memory in use.
Info: Finished startup with 0 kB of memory in use.
TCL: Minimizing for 1000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2
TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 0.0607 -1.#IND 0.0000
0.0000 -11.8639 -247.8474 0.0000
0.0000 0.0000 -1.#IND 0.0000
-1.#IND -1.#IND 0.0000 -1.#IND
-1.#IND 46656.0000 -1.#IND -1.#IND
INITIAL STEP: 1e-006
GRADIENT TOLERANCE: -1.#IND
############### LINUX ###############
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6b1 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 50900 for net-linux-iccstatic
Info: Built Fri Jul 29 11:30:30 CDT 2005 by jim on kyoto.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.6b1 Linux-i686 1 delta1 uno
Info: Running on 1 processors.
Info: 7723 kB of memory in use.
Info: Configuration file is min_solv.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 36 0 0
Info: PERIODIC CELL BASIS 2 0 36 0
Info: PERIODIC CELL BASIS 3 0 0 36
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM 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: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME sim_out.dcd
Info: DCD FREQUENCY 10
Info: DCD FIRST STEP 10
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME sim_out
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14.5
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 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 17
Info: ENERGY OUTPUT STEPS 1000
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1150733713
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB mixture.pdb
Info: STRUCTURE FILE mixture.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 1 BONDS
Info: 1 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 2 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 900 ATOMS
Info: 600 BONDS
Info: 300 ANGLES
Info: 0 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 EXCLUSIONS
Info: 2697 DEGREES OF FREEDOM
Info: 900 HYDROGEN GROUPS
Info: TOTAL MASS = 13202.7 amu
Info: TOTAL CHARGE = 0 e
Info: *****************************
Info: Entering startup phase 0 with 7943 kB of memory in use.
Info: Entering startup phase 1 with 7943 kB of memory in use.
Info: Entering startup phase 2 with 8047 kB of memory in use.
Info: Entering startup phase 3 with 8054 kB of memory in use.
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.289994 -0.0983423 -0.125683
Info: LARGEST PATCH (6) HAS 117 ATOMS
Info: Entering startup phase 4 with 8195 kB of memory in use.
Info: Entering startup phase 5 with 8195 kB of memory in use.
Info: Entering startup phase 6 with 8195 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 8196 kB 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 12.0805
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04308e-13 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2.75 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 6656 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.055e-15 AT 0.0441942
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 7.45058e-09 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 7.62939e-06 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
Info: Entering startup phase 8 with 8713 kB of memory in use.
Info: Finished startup with 9867 kB of memory in use.
TCL: Minimizing for 1000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2
TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 0.0607 0.0056 0.0000
0.0000 -11.8639 -247.8474 0.0000
0.0000 0.0000 -259.6450 0.0000
-259.6450 -259.6450 0.0000 99999999.9999
99999999.9999 46656.0000 99999999.9999 99999999.9999
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 6.25e-08
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 1.5625e-08
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 3.90625e-09
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 9.76562e-10
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 2.44141e-10
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 6.10352e-11
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 1.52588e-11
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 3.8147e-12
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 9.53674e-13
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 2.38419e-13
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 5.96046e-14
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 1.49012e-14
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 3.72529e-15
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 9.31323e-16
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 2.32831e-16
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 5.82077e-17
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION
INITIAL STEP: 1.45519e-17
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