Re: Angle CO2 Problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jun 16 2006 - 10:08:04 CDT

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
************************************************

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