Re: about extrabonds restrain

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 30 2011 - 08:06:04 CDT

On Mon, Aug 29, 2011 at 5:22 PM, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> Hi All,
>
> I tried to use extrabonds to restrain some dihedral angles in my system, I copied my input and output file here, but I did not see any related information of extrabonds in the output file before the minimization began. so I was wondering if I used this command correctly.

hi emilia,

according to your output, you have bigger fish to fry: your VDW energy
is ballooning
which is indication of either bad box dimensions or bad contacts in your system.
before worrying about extrabonds, i would resolve that first.

cheers,
    axel.

> Thanks a lot!
>
>
>
> Input file:
> -----------------------------------------------------------------------------
> set temp 303.15
> set a 40.9878
> set b 40.9878
> set c 70
> set zcen 0.0
>
> #Can get this from ?xtla parameter of last frame in the
> #charmm trajectory.
>
> structure step5_assembly.xplor.psf
> coordinates step5_assembly.pdb
> temperature 0
> parameters par_all27pl36.prm
> paraTypeCharmm on
>
> outputEnergies  1000
> outputTiming    1000
> xstFreq         1000
> dcdFreq         1000
> wrapWater       on
> wrapAll         on
> wrapNearest     off
>
> rigidbonds      all
> timestep        1
> nonBondedFreq   1
> fullElectFrequency 1
> stepsPerCycle   20
>
> switching       on
> switchDist      10.0
> cutoff          12.0
> pairlistdist    16.0
>
> outputname step6.1_equilibration
> binaryoutput on
>
> restartname step6.1_equilbration
> restartfreq 1000
>
> numsteps 90000000
>
> #########################################
>
> cellBasisVector1     $a   0.0   0.0;   # vector to the next image
> cellBasisVector2    0.0    $b   0.0;
> cellBasisVector3    0.0   0.0    $c;
> cellOrigin          0.0   0.0 $zcen;   # the *center* of the cell
>
> #########################################
> Pme             yes
> PmeInterpOrder    6
> Pme             yes
> PmeInterpOrder    6
> PmeGridsizeX     48
> PmeGridsizeY     48
> PmeGridsizeZ     78
>
> exclude         scaled1-4
> 1-4scaling      1.0
>
> ########################################
> # PRESSURE AND TEMPERATURE CONTROL
> #########################################
>
> langevin                on
> langevinDamping         10
> langevinTemp            $temp
> langevinHydrogen        no
>
> #langevinPiston          on
> #langevinPistonTarget    1.01325
> #langevinPistonPeriod    50.0
> #langevinPistonDecay     25.0
> #langevinPistonTemp      $temp
>
> useGroupPressure        yes     #THIS WILL ALLOW THE SYSTEM SMALLER FLUCTUATIONS
>
> #useFlexibleCell yes
>
>
> ### For the Dihedarl Angles Restraint####
> extraBonds yes
> extraBondsFile dihe.txt
>
>
> #########################################
> #Minimize
> #########################################
> minimize 10000
>
>
> ------------------------------------------------------------------------------------
>
>
>
> Output file:
> --------------------------------------------------------------------------------------
> Charm++: standalone mode (not using charmrun)
> Charm++> scheduler running in netpoll mode.
> Charm++> Running on 1 unique compute nodes (8-way SMP).
> Charm++> cpu topology info is gathered in 0.001 seconds.
> Info: NAMD 2.8 for Linux-x86_64
> 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 60303 for net-linux-x86_64-iccstatic
> Info: Built Sat May 28 11:28:04 CDT 2011 by jim on nereid.ks.uiuc.edu
> Info: 1 NAMD  2.8  Linux-x86_64  1    login.bioinformatics.ku.edu  emiliawu
> Info: Running on 1 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.00426984 s
> Info: 1.49535 MB of memory in use based on CmiMemoryUsage
> Info: Configuration file is step6.1_equilibration.namd.inp
> Info: Working in the current directory /home2/emiliawu/NAMD_Equilibration/NAMD_TestRun
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP               1
> Info: NUMBER OF STEPS        90000000
> Info: STEPS PER CYCLE        20
> Info: PERIODIC CELL BASIS 1  40.9878 0 0
> Info: PERIODIC CELL BASIS 2  0 40.9878 0
> Info: PERIODIC CELL BASIS 3  0 0 70
> 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: MIN ATOMS PER PATCH    40
> Info: INITIAL TEMPERATURE    0
> 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           step6.1_equilibration.dcd
> Info: DCD FREQUENCY          1000
> Info: DCD FIRST STEP         1000
> Info: DCD FILE WILL CONTAIN UNIT CELL DATA
> Info: XST FILENAME           step6.1_equilibration.xst
> Info: XST FREQUENCY          1000
> Info: NO VELOCITY DCD OUTPUT
> Info: NO FORCE DCD OUTPUT
> Info: OUTPUT FILENAME        step6.1_equilibration
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: RESTART FILENAME       step6.1_equilbration
> Info: RESTART FREQUENCY      1000
> Info: BINARY RESTART FILES WILL BE USED
> Info: 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                 0
> Info: HYDROGEN GROUP CUTOFF  2.5
> Info: PATCH DIMENSION        18.5
> Info: ENERGY OUTPUT STEPS    1000
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS    1000
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE   303.15
> Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> 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         48 48 78
> Info: PME MAXIMUM GRID SPACING    1.5
> Info: Attempting to read FFTW data from FFTW_NAMD_2.8_Linux-x86_64.txt
> Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
> Info: Writing FFTW data to FFTW_NAMD_2.8_Linux-x86_64.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     1314652391
> Info: USE HYDROGEN BONDS?    NO
> Info: COORDINATE PDB         step5_assembly.pdb
> Info: STRUCTURE FILE         step5_assembly.xplor.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS             par_all27pl36.prm
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SUMMARY OF PARAMETERS:
> Info: 308 BONDS
> Info: 803 ANGLES
> Info: 1326 DIHEDRAL
> Info: 74 IMPROPER
> Info: 6 CROSSTERM
> Info: 191 VDW
> Info: 0 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> Warning: Ignored 1795 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: 0.961706
> Info: READING EXTRA BONDS FILE dihe.txt
> Info: READ 48 EXTRA DIHEDRALS
> Info: READ 48 EXTRA IMPROPERS
> Info: TIME FOR READING PDB FILE: 0.119285
> Info:
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 13603 ATOMS
> Info: 11822 BONDS
> Info: 17851 ANGLES
> Info: 23352 DIHEDRALS
> Info: 144 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 10425 RIGID BONDS
> Info: 30384 DEGREES OF FREEDOM
> Info: 4973 HYDROGEN GROUPS
> Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
> Info: 4973 MIGRATION GROUPS
> Info: 4 ATOMS IN LARGEST MIGRATION GROUP
> Info: TOTAL MASS = 78474.9 amu
> Info: TOTAL CHARGE = 2.14577e-06 e
> Info: MASS DENSITY = 1.10811 g/cm^3
> Info: ATOM DENSITY = 0.115672 atoms/A^3
> Info: *****************************
> Info:
> Info: Entering startup at 1.2277 s, 6.22298 MB of memory in use
> Info: Startup phase 0 took 0.000192881 s, 6.22307 MB of memory in use
> Info: Startup phase 1 took 0.0365031 s, 9.63379 MB of memory in use
> Info: Startup phase 2 took 0.000496864 s, 9.77008 MB of memory in use
> Info: Startup phase 3 took 0.000142097 s, 9.76996 MB of memory in use
> Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 3 (PERIODIC)
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0 0 0
> Info: LARGEST PATCH (4) HAS 1321 ATOMS
> Info: Startup phase 4 took 0.012202 s, 11.6251 MB of memory in use
> Info: PME using 1 and 1 processors for FFT and reciprocal sum.
> Info: PME GRID LOCATIONS: 0
> Info: PME TRANS LOCATIONS: 0
> Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
> Info: Startup phase 5 took 0.00214601 s, 12.3358 MB of memory in use
> Info: Startup phase 6 took 0.000154972 s, 12.3357 MB of memory in use
> LDB: Central LB being created...
> Info: Startup phase 7 took 0.000184059 s, 12.3372 MB of memory in use
> Info: CREATING 234 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> Info: Startup phase 8 took 0.00867581 s, 14.5526 MB of memory in use
> Info: Startup phase 9 took 0.000387192 s, 16.1929 MB of memory in use
> Info: Finished startup at 1.28878 s, 16.1929 MB of memory in use
>
> TCL: Original numsteps 90000000 will be ignored.
> TCL: Minimizing for 10000 steps
> ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
>
> ENERGY:       0       953.7261      5194.3471      3377.7824       121.6505         -17566.9499 9999999999.9999         0.0000         0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999 9999999999.9999         0.0000      9999999999.9999 9999999999.9999    117599.9824 9999999999.9999 9999999999.9999
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING 4059 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY:       1      4387.1966      7004.3677      3638.6117       146.6604         -17928.3686 9999999999.9999         0.0000         0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999 9999999999.9999         0.0000      9999999999.9999 9999999999.9999    117599.9824 9999999999.9999 9999999999.9999
>
> MINIMIZER SLOWLY MOVING 3599 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY:       2     13145.3144     11561.9034      4191.7499       229.0004         -18070.9888 9999999999.9999         0.0000         0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999 9999999999.9999         0.0000      9999999999.9999 9999999999.9999    117599.9824 9999999999.9999 9999999999.9999
>
> MINIMIZER SLOWLY MOVING 3104 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY:       3     25350.7586     17790.1699      5003.3345       329.2088         -17687.1734 9999999999.9999         0.0000         0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999 9999999999.9999         0.0000      9999999999.9999 9999999999.9999    117599.9824 9999999999.9999 9999999999.9999
>
> MINIMIZER SLOWLY MOVING 2675 ATOMS WITH BAD CONTACTS DOWNHILL
> ENERGY:       4     39253.1703     24983.6378      5895.5457       435.2309         -17595.3231 9999999999.9999         0.0000         0.0000         0.0000      9999999999.9999         0.0000 9999999999.9999 9999999999.9999         0.0000      9999999999.9999 9999999999.9999    117599.9824 9999999999.9999 99999
>
> --------------------------------------------------------------------------------------
>
>
> Emilia
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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