Re: Angle CO2 Problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jun 16 2006 - 10:28:49 CDT

Setting the force to 0 will always work, there will be no penalty.
Measure how long a CO2 molecule is in your pdb file just as a sanity
check. Remember that adding 2A to your box size actually adds only 1A per
edge. Its worth just adding 5 to see what happens.

Also, why are you using such large K values for the bonds and angles? Is
there IR data to suggest such a large force constant in the angles?

I am still puzzled by the lack of memory reporting by NAMD upon startup of
each phase.

Brian

On Fri, 16 Jun 2006, linefinc wrote:

> The box is 2A greater the solvent size (35 solvent 37 box) !
> If I set Ktheta to 0 the simulation "work"
> The machines is a P4 1GB Ram win XP bat if the simulation work i use a
> 8 Processor Opteron!
>
> TNX
> Sassaro
>
>
> 2006/6/16, Brian Bennion <brian_at_youkai.llnl.gov>:
>> Hello,
>>
>> Its not just the angles that are messed up, but it appears that a bond is
>> being cut in half by the box. This will also give weird angle results.
>>
>> Try increasing the box size a bit for the minimization.
>>
>> One more interesting thing, all the namd phases are using OKB of memory.
>> This is odd. What type of machine are you running your namd on?
>>
>>
>> Brian
>>
>> On Fri, 16 Jun 2006, linefinc wrote:
>>
>> > Hi all
>> >
>> > I have made a solvent box with CO2 bat I have problem with angle!
>> >
>> > 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 304921.5560 -1.#IND 0.0000
>> > 0.0000 0.0000 14859825.8105 0.0000
>> > 0.0000 0.0000 -1.#IND 0.0000
>> > -1.#IND -1.#IND 0.0000 -1.#IND
>> > -1.#IND 50653.0000 -1.#IND -1.#IND
>> >
>> > INITIAL STEP: 1e-006
>> > GRADIENT TOLERANCE: -1.#IND
>> >
>> > I have remade Solvent Box , Topology , Potential and namd script bat
>> > always the same error!
>> >
>> > Where's the error ?
>> >
>> > Thanks
>> >
>> > Sassaro
>> >
>> >
>> ----------------------------------------------Topology--------------------------------------------
>> >
>> > !
>> > 27 1
>> >
>> >
>> > MASS 1 HA 1.00800 ! H idorgeno non polare
>> > MASS 2 CA 12.01100 ! C Aromatico
>> > MASS 3 CT3 12.01100 ! CH3
>> > MASS 4 CT2 12.01100 ! CH2
>> > MASS 5 CT1 12.01100 ! CH1
>> > MASS 6 N 14.00700 ! N
>> > MASS 7 O 15.99900 ! O
>> > MASS 8 Cl 35.453 ! Cloro
>> > MASS 9 C 12.01100 ! C del C=O
>> >
>> >
>> > !AUTO ANGLES DIHE
>> >
>> >
>> > RESI CO2 0.00 ! Tetra cloruro di carbonio
>> > GROUP
>> > ATOM C1 C 0.863134 ! 0
>> > ATOM O1 O -0.431567 ! 0
>> > ATOM O2 O -0.431567 ! 0
>> >
>> > DOUBLE O1 C1 ! 0 -> 1
>> > DOUBLE O2 C1 ! 0 -> 2
>> >
>> >
>> > ---------------------------------------------- Parameter
>> > --------------------------------------------
>> >
>> > *>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<<
>> > *>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
>> > *from
>> > *>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
>> > *>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>> > *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>> > *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
>> > *and
>> > * \\\\\\\ CHARMM27 All-Hydrogen Lipid Parameter File ///////
>> > * \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
>> > * Alexander D. MacKerell Jr.
>> > * August 1999
>> > * All comments to ADM jr. email:alex,mmiris.ab.umd.edu
>> > * telephone: 410-706-7442
>> > *
>> >
>> >
>> >
>> > BONDS
>> > !
>> > !V(bond) = Kb(b - b0)**2
>> > !
>> > !Kb: kcal/mole/A**2
>> > !b0: A
>> > !
>> > !atom type Kb b0
>> > !
>> > O C 620.000 1.161 ! ALLOW PEP POL ARO 1.80
>> >
>> >
>> > ANGLES
>> >
>> > !
>> > !V(angle) = Ktheta(Theta - Theta0)**2
>> > !
>> > !V(Urey-Bradley) = Kub(S - S0)**2
>> > !
>> > !Ktheta: kcal/mole/rad**2
>> > !Theta0: degrees
>> > !Kub: kcal/mole/A**2 (Urey-Bradley)
>> > !S0: A
>> > !
>> > !atom types Ktheta Theta0 Kub S0
>> > !
>> > O C O 620.0 180.000 ! dovrebbe essere 80
>> >
>> > NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>> > cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
>> > ! !adm jr., 5/08/91, suggested cutoff scheme
>> > !
>> > !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
>> > !
>> > !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
>> > !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
>> > !
>> > !atom ignored epsilon Rmin/2 ignored eps,1-4
>> Rmin/2,1-4
>> > !
>> > C 0.000000 -0.110000 2.000000 !
>> > O 0.000000 -0.120000 1.700000 0.000000 -0.120000
>> 1.400000 !
>> >
>> > END
>> >
>> > ---------------------------------------------- Namd Script
>> > --------------------------------------------
>> >
>> >
>> > #############################################################
>> > ## JOB DESCRIPTION ##
>> > #############################################################
>> >
>> > # Ricerca della corretta ottimizzazione
>> > #
>> > #
>> >
>> > #############################################################
>> > ## ADJUSTABLE PARAMETERS ##
>> > #############################################################
>> >
>> > structure mixture.psf
>> > coordinates mixture.pdb
>> >
>> > set temperature 300
>> >
>> > set outputname sim
>> >
>> > firsttimestep 0
>> >
>> >
>> > #############################################################
>> > ## SIMULATION PARAMETERS ##
>> > #############################################################
>> >
>> > # Input
>> > paraTypeCharmm on
>> > parameters par_all27_prot_lipid.prm
>> > temperature $temperature
>> >
>> > # Periodic Boundary conditions
>> > cellBasisVector1 37.0 0.0 0.0
>> > cellBasisVector2 0.0 37.0 0.0
>> > cellBasisVector3 0.0 0.0 37.00
>> > wrapAll on
>> > cellOrigin 0. 0. 0.
>> >
>> > # Force-Field Parameters
>> > exclude scaled1-4
>> > 1-4scaling 1.0
>> > cutoff 12.
>> > switching on
>> > switchdist 10.
>> > pairlistdist 14.5
>> >
>> >
>> > # Integrator Parameters
>> > timestep 1 ;# 1fs/step
>> > nonbondedFreq 2
>> > fullElectFrequency 4
>> > stepspercycle 20
>> >
>> >
>> > # Constant Temperature Control
>> > #langevin on ;# do langevin dynamics
>> > #langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>> > #langevinTemp $temperature
>> > #langevinHydrogen no ;# don't couple langevin bath to hydrogens
>> >
>> > # Output
>> >
>> > outputName sim_out
>> >
>> > #restartfreq 1000 ;# 10000 step = every 1ps
>> > dcdfreq 100
>> > outputEnergies 100
>> > #outputPressure 500
>> >
>> >
>> >
>> > #rigidBonds all
>> >
>> > # Fixed Atoms Constraint (set PDB occupancy-column to 1)
>> > fixedAtoms no
>> >
>> > #############################################################
>> > ## EXTRA PARAMETERS ##
>> > #############################################################
>> >
>> > minimize 1000
>> >
>> >
>> > # run MD
>> > run 500000 ;# 20ps
>> >
>> > ---------------------------------------------- Completa Namd OUT
>> > --------------------------------------------
>> >
>> > 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: 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 37 0 0
>> > Info: PERIODIC CELL BASIS 2 0 37 0
>> > Info: PERIODIC CELL BASIS 3 0 0 37
>> > 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 0
>> > 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: CONJUGATE GRADIENT MINIMIZATION ACTIVE
>> > Info: LINE MINIMIZATION GOAL = 0.0001
>> > Info: BABY STEP SIZE = 0.01
>> > Info: TINY STEP SIZE = 1e-006
>> > 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 1150455511
>> > 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 0 0
>> > Info: LARGEST PATCH (7) HAS 123 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 304921.5560 -1.#IND 0.0000
>> > 0.0000 0.0000 14859825.8105 0.0000
>> > 0.0000 0.0000 -1.#IND 0.0000
>> > -1.#IND -1.#IND 0.0000 -1.#IND
>> > -1.#IND 50653.0000 -1.#IND -1.#IND
>> >
>> > INITIAL STEP: 1e-006
>> > GRADIENT TOLERANCE: -1.#IND
>> >
>>
>> ************************************************
>> Brian Bennion, Ph.D.
>> Biosciences Directorate
>> Lawrence Livermore National Laboratory
>> P.O. Box 808, L-448 bennion1_at_llnl.gov
>> 7000 East Avenue phone: (925) 422-5722
>> Livermore, CA 94550 fax: (925) 424-5513
>> ************************************************
>>
>>
>

************************************************
   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-448 bennion1_at_llnl.gov
   7000 East Avenue phone: (925) 422-5722
   Livermore, CA 94550 fax: (925) 424-5513
************************************************

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