problems with simulation of LJ fluid

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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