From: linefinc (linefinc_at_gmail.com)
Date: Wed Jun 14 2006 - 09:58:58 CDT
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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