From: 翁林岽 (wenglindong_at_yahoo.com.cn)
Date: Sat Dec 01 2012 - 17:30:28 CST
Hi, NAMDers,
Is there anyone who ever simulated Lennard Jones fluids, especially pure Ar or pure Kr, using NAMD? I tried to do so, but got wrong results for Ar/Kr mixtures and even could not run the equilibrium of pure Kr or pure Ar fluids. Attached is the top, par, conf files, any suggestions would be really appreciated.
Topology file:
!Ar/Kr
MASS 1 AR 39.948000 AR !
MASS 2 KR 83.798000 KR !
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS
RESI ARLJ 0.00 ! Ar Atom
GROUP
ATOM AR1 AR 0.00
PATCHING FIRST NONE LAST NONE
RESI KRLJ 0.00 ! Kr Atom
GROUP
ATOM KR1 KR 0.00
PATCHING FIRST NONE LAST NONE
END
Parameter file:
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
!
! ions, note lack of NBFIXes
!
AR 0.0 -0.2381 1.91099 ! Ar
KR 0.0 -0.3319 2.03895 ! Kr
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
! READ PARAM APPEND CARD
! to append hbond parameters from the file: par_hbond.inp
END
Config file:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of a Kr Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure kr_b.psf
coordinates kr_b.pdb
set temperature 94.4 ;# K
set outputname kr_b
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
temperature $temperature ;# initialize velocities randomly
firsttimestep 0
# Force-Field Parameters
paraTypeCharmm on
parameters par_lj.prm
exclude scaled1-4
1-4scaling 1.0
# You have some freedom choosing the cutoff
cutoff 12. ;# may use smaller, maybe 10, with PME
switching on
switchdist 10. ;# cutoff - 2
pairlistdist 13.5 ;# > cutoff
# Integrator Parameters
timestep 2.0 ;# 2 fs/step
rigidBonds all ;# needed for 2 fs steps
nonbondedFreq 1 ;# nonbonded forces every step (>= 2 fs, here one step)
fullElectFrequency 2 ;# PME only every other step
stepspercycle 10 ;# redo pairlists every ten steps
# Constant Temperature Control
langevin on ;# langevin dynamics
langevinTemp $temperature ;# random noise at this level
langevinDamping 5. ;# damping coefficient of 5 1/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control
useGroupPressure yes ;# require periodic boundary conditions
useFlexibleCell no ;# no for isotropic system, yes for anisotropic one
useConstantRatio no ;# no for isotropic system, yes for anisotropic one
useConstantArea no ;# no for isotropic system, yes for anisotropic one
# (Should be accompanied by Langevin dynamics for temperature control)
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 100. ;# oscillation period around 100 fs
LangevinPistonDecay 50. ;# oscillation decay time of 50 fs
LangevinPistonTemp $temperature ;# equal to the controlled temperature
# Periodic Boundary Conditions
cellBasisVector1 32. 0. 0.
cellBasisVector2 0. 32. 0.
cellBasisVector3 0. 0. 32.
cellOrigin 0. 0. 0.
wrapAll on ;# wrap all molecules
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
# Output
outputName $outputname
restartfreq 1000 ;# 1000 steps = every 2 ps
dcdfreq 10
velDCDfreq 10
xstFreq 500
outputEnergies 500 ;# 500 steps = every 1 ps
outputTiming 500 ;# shows time per step and time to completion
outputPressure 500
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 10000 ;# lower potential energy for 10000 steps (20 ps)
reinitvels $temperature ;# since minimization zeros velocities
run 500000 ;# 1 ns
The wrong information about the simulation of pure Kr fluids is:
... ...
LINE MINIMIZER BRACKET: DX 4.08248e-302 3.67423e-301 DU 0 0 DUDX -2.21951e+11 -2.21951e+11 -2.21951e+11
LINE MINIMIZER REDUCING GRADIENT FROM 3.32927e+11 TO 3.32927e+08
PRESSURE: 10000 1.00128e+06 7032.42 -16055.9 7032.42 1.37011e+06 -28789.2 -16055.9 -28789.2 4.01709e+06
GPRESSURE: 10000 1.00128e+06 7032.42 -16055.9 7032.42 1.37011e+06 -28789.2 -16055.9 -28789.2 4.01709e+06
TIMING: 10000 CPU: 655.735, 0.0628918/step Wall: 655.735, 0.0628918/step, 0 hours remaining, 726.261719 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 10000 0.0000 0.0000 0.0000 0.0000 0.0000 9999999999.9999 0.0000 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000 2129495.3815 2129495.3815 32768.0000 2129495.3815 2129495.3815
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
WRITING COORDINATES TO DCD FILE AT STEP 10000
WRITING COORDINATES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO DCD FILE AT STEP 10000
WRITING VELOCITIES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 10000 TO 94.4 KELVIN.
TCL: Running for 500000 steps
PRESSURE: 10000 1.03964e+06 6761.74 -21242.5 6761.74 1.46064e+06 -106189 -21242.5 -106189 5.06431e+06
GPRESSURE: 10000 1.03964e+06 6761.74 -21242.5 6761.74 1.46064e+06 -106189 -21242.5 -106189 5.06431e+06
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 10000 0.0000 0.0000 0.0000 0.0000 0.0000 9999999999.9999 0.0000 0.0000 206.8176 9999999999.9999 95.1763 9999999999.9999 9999999999.9999 95.1763 2521528.8179 2521528.8179 32768.0000 2521528.8179 2521528.8179
ERROR: Atom 12 velocity is 1.03923e+12 -3.01387e+11 -7.6917e+11 (limit is 6000, atom 0 of 257 on patch 0 pe 8)
ERROR: Atom 28 velocity is 126.522 -1146.48 12682.8 (limit is 6000, atom 3 of 257 on patch 0 pe 8)
ERROR: Atom 55 velocity is -1.50636e+11 -2.28264e+11 3.73979e+11 (limit is 6000, atom 10 of 257 on patch 0 pe 8)
ERROR: Atom 180 velocity is 10799 483020 1.23976e+06 (limit is 6000, atom 35 of 257 on patch 0 pe 8)
... ...
ERROR: Atom 19 velocity is -1.27025e+11 6.85185e+11 6.58609e+11 (limit is 6000, atom 223 of 232 on patch 2 pe 4)
ERROR: Atom 27 velocity is 1.27025e+11 -6.85185e+11 -6.58609e+11 (limit is 6000, atom 224 of 232 on patch 2 pe 4)
ERROR: Atom 109 velocity is -1.01188e+12 1.09255e+12 -2.67297e+11 (limit is 6000, atom 226 of 232 on patch 2 pe 4)
ERROR: Atom 117 velocity is 1.01188e+12 -1.09255e+12 2.67297e+11 (limit is 6000, atom 227 of 232 on patch 2 pe 4)
ERROR: Atom 684 velocity is -110.949 -691.142 -13593.1 (limit is 6000, atom 229 of 232 on patch 2 pe 4)
ERROR: Atoms moving too fast; simulation has become unstable (62 atoms on patch 2 pe 4).
ERROR: Exiting prematurely; see error messages above.
====================================================
Lindong
COE
University of North Carolina at Charlotte
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