about extrabonds restrain

From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Mon Aug 29 2011 - 16:22:53 CDT

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.
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

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