From: linefinc (linefinc_at_gmail.com)
Date: Thu Jun 15 2006 - 03:47:19 CDT
Hi
I have made a slightly smalle box (35... ) and VdW work correct!
In the PARAMETER FILES i have add the row :
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
O C 620.000 1.800 !
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 80.000 180.000 !
If I set Ktheta to 0 it word bat don't calc correctly the ANGLES energy:
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 125137.0204 0.0000 0.0000
0.0000 0.0000 7354783.1455 0.0000
0.0000 0.0000 7479920.1659 0.0000
7479920.1659 7479920.1659 0.0000 40654979.6484
40654979.6484 50653.0000 40654979.6484 40654979.6484
INITIAL STEP: 1e-006
GRADIENT TOLERANCE: 5.04696e+008
ENERGY: 1 128277.6519 0.0000 0.0000
0.0000 0.0000 306007.2450 0.0000
0.0000 0.0000 434284.8968 0.0000
434284.8968 434284.8968 0.0000 1937022.2661
1937022.2661 50653.0000 1937022.2661 1937022.2661
ENERGY: 2 130649.0810 0.0000 0.0000
0.0000 0.0000 164182.4216 0.0000
0.0000 0.0000 294831.5026 0.0000
294831.5026 294831.5026 0.0000 1151993.7537
1151993.7537 50653.0000 1151993.7537 1151993.7537
ENERGY: 3 131911.7652 0.0000 0.0000
0.0000 0.0000 261092.9611 0.0000
0.0000 0.0000 393004.7263 0.0000
393004.7263 393004.7263 0.0000 1673700.3769
1673700.3769 50653.0000 1673700.3769 1673700.3769
if I set Ktheta to other positive value from 1 at 100 it don't work :
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 125137.0204 -1.#IND 0.0000 0.0000
0.0000 7354783.1455 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
thanks
Sassaro
2006/6/14, Leandro Martínez <leandromartinez98_at_gmail.com>:
>
> Hi Sassaro,
> It seems that you have two problems there. One is that the angle parameters
> seem to be wrong, since this #IND appears in the angle contribution to the
> energy. Another one is the fact that the VDW energy of the system is
> 999999999. This is not usual if you are using packmol, particularly for
> system with that low density. When using periodic boundary conditions it may
> happen that two molecules get overlaped in the interface between the boxes
> (since packmol does not use periodic boundary conditions). This can be
> solved by packing your molecules in a slightly smaller box (35x35x35, for
> example), and running the simulation in the actual box (36x36x36). This will
> guarantee that no overlap occurs due to the periodic boundary. Nevertheless,
> the minimization should take care of this problem for the box you have, the
> problem is that it is failling due to the problem in the angle parameters.
> Best regards,
> Leandro.
>
>
>
>
> On 6/14/06, linefinc <linefinc_at_gmail.com> wrote:
> > Hi
> >
> > I work on a simulation of supercritical CO2 bat I have same problem.
> > I generate the solvent box with packmol. The solvent box is a cubic
> > box 36x36x36 with 300 molecules of CO2. I generate with success the
> > pdb e psf with psfgen. When i run namd it told me this below. I can't
> > expand the box.
> >
> > thanks
> >
> > Sassaro
> >
> > 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 0.01
> > Info: NUMBER OF STEPS 0
> > Info: STEPS PER CYCLE 20
> > Info: PERIODIC CELL BASIS 1 36 0 0
> > Info: PERIODIC CELL BASIS 2 0 36 0
> > Info: PERIODIC CELL BASIS 3 0 0 36
> > 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 200
> > Info: DCD FIRST STEP 200
> > 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: RESTART FILENAME sim_out.restart
> > 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 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 10
> > Info: LANGEVIN DYNAMICS ACTIVE
> > Info: LANGEVIN TEMPERATURE 0
> > Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> > Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> > 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 1150296712
> > 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: 188 BONDS
> > Info: 455 ANGLES
> > Info: 547 DIHEDRAL
> > Info: 49 IMPROPER
> > Info: 89 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: 2700 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 136 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 37.1883 -1.#IND 0.0000
> > 0.0000 0.0000 99999999.9999 0.0000
> > 0.0000 0.0000 -1.#IND 0.0000
> > -1.#IND -1.#IND 0.0000 -1.#IND
> > -1.#IND 46656.0000 -1.#IND -1.#IND
> >
> > INITIAL STEP: 1e-006
> > GRADIENT TOLERANCE: -1.#IND
> >
> > Config File:
> >
> >
> #############################################################
> > ## JOB DESCRIPTION
> ##
> >
> #############################################################
> >
> > # Ricerca della corretta ottimizzazione
> > #
> > #
> >
> >
> #############################################################
> > ## ADJUSTABLE PARAMETERS
> ##
> >
> #############################################################
> >
> > structure mixture.psf
> > coordinates mixture.pdb
> >
> > set temperature 0
> >
> > set outputname sim
> >
> > firsttimestep 0
> >
> >
> >
> #############################################################
> > ## SIMULATION PARAMETERS
> ##
> >
> #############################################################
> >
> > # Input
> > paraTypeCharmm on
> > parameters par_all27_prot_lipid.prm
> > temperature $temperature
> >
> > # Periodic Boundary conditions
> > cellBasisVector1 36.0 0.0 0.0
> > cellBasisVector2 0.0 36.0 0.0
> > cellBasisVector3 0.0 0.0 36.00
> > 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 0.01 ;# 0.01fs/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
> >
> > #LangevinPiston on ;
> > #LangevinPistonTarget 150 ;#150 abar
> > #LangevinPistonPeriod 200;
> > #LangevinPistonDecay 100;
> > #LangevinPistonTemp $temperature;
> >
> > # Output
> >
> > outputName sim_out
> >
> > restartfreq 1000 ;# 10000 step = every 1ps
> > dcdfreq 200
> > outputEnergies 10
> >
> >
> > # Fixed Atoms Constraint (set PDB occupancy-column to 1)
> > fixedAtoms no
> >
> >
> #############################################################
> > ## EXTRA PARAMETERS
> ##
> >
> #############################################################
> >
> > # Minimization
> > minimize 1000
> >
> > # run MD
> > run 5000
> >
>
>
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