From: linefinc (linefinc_at_gmail.com)
Date: Fri Jun 16 2006 - 06:08:23 CDT
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
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