RE: Angle 2, Where is the problem [IMPORTANT]

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jun 20 2006 - 01:00:09 CDT

Your cellOrigin is set incorrectly in your .conf file. I measured this in
VMD:

measure center $sel
18.00963974 17.9956378937 17.9846000671

Try changing that and let us know if it fixes it or not.

As for the differences between Windows and Linux, both are numerical errors
so it's not so surprising really.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of linefinc
Sent: Monday, June 19, 2006 11:51 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Angle 2, Where is the problem [IMPORTANT]

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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