From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 30 2011 - 01:18:37 CDT
Hi,
why does no people use the manual? ^^
Well the extrabonds command can be used with an extrabonds file, this file
is build like this, please correct me if I don't remember correctly.
10 12 4.6 10
Where the 1st and 2nd column are atom index (beginning by 0) which should be
bond together. 3rd column is bond length and last column is force constant
of the virtual bond to hold the bond length with.
Hope that helps
Norman Geist.
-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Ling Wu
Gesendet: Montag, 29. August 2011 23:23
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: about extrabonds restrain
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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