AW: AW: about extrabonds restrain

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Aug 31 2011 - 00:05:47 CDT

Oh sorry.

well as others already pointed out, there seems to be something wrong with
your initial structure. Try running without the extrabonds to see if the
problem with high initial energies is still there. I would think about two
things:

1. Maybe you have just a bad initial structure, and should try to minimize
this. Everythings fine.
2. Maybe you have built your extrabonds file in a way, or use additional
fixed atoms, that tell namd to handle your structure in a way that it can't
get rid of. For example you maybe try to put angles that the system
deprecates. This would meen the problem would not occur without the
extrabonds. If that’s true, you should see if your angles in extrabonds file
are right.

Best wishes

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: Dienstag, 30. August 2011 14:58
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: AW: namd-l: about extrabonds restrain

Hi Norman,

Thanks a lot for your reply, but I did read the manual and prepared the
corresponding file dihe.txt, the file is like this
dihedral 1081 1084 1086 1088 250. 0.
dihedral 1215 1218 1220 1222 250. 0.
dihedral 1349 1352 1354 1356 250. 0.
dihedral 1483 1486 1488 1490 250. 0.
dihedral 1617 1620 1622 1624 250. 0.
dihedral 1751 1754 1756 1758 250. 0.
dihedral 1885 1888 1890 1892 250. 0.
dihedral 2019 2022 2024 2026 250. 0.
dihedral 2153 2156 2158 2160 250. 0.
dihedral 2287 2290 2292 2294 250. 0.
dihedral 2421 2424 2426 2428 250. 0.
dihedral 2555 2558 2560 2562 250. 0.
dihedral 2689 2692 2694 2696 250. 0.
dihedral 2823 2826 2828 2830 250. 0.
dihedral 2957 2960 2962 2964 250. 0.
dihedral 3091 3094 3096 3098 250. 0.
dihedral 3225 3228 3230 3232 250. 0.

Since this file is kind of long, I did not copy it with my input and output
files yesterday. sorry about that.
So do you know what's going on here?

Emilia

On Aug 30, 2011, at 1:18 AM, Norman Geist wrote:

> 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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