From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Tue Jun 20 2006 - 01:15:37 CDT
Hi there,
I quickly went through your files.
As far as I see your molecules are perfectly linear and this may create
problems in the calculation of the potential energy (bond angle potential).
As a matter of fact, if you put to zero the value of Ktheta in the
parameters file you will see that your simulation will start correctly.
In conclusion, a quick solution if you want to use these initial
coordinates might be to run a short minimization (100 steps or less)
using Ktheta=0 then you can use the newly-obtained coordinates to start
your simulation putting back Ktheta to its right value.
Giovanni
> 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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