Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both systems below. The barostats are different but I don't think this is the cause. I think that one worked because of the cut-off specifications (rlist, rvdw and rcoulomb), but I am not sure of the explanation of how the cut-off values can influence the shape of a pair distribution function. The fourier spacing in both parameter files are also different. Please, if someone knows how these cut-off values and maybe fourier spacing could influence the shape of a pair distribution function, let me know the explanation.
.mdp file which gave the plot which converges to zero: title = NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 500000 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 500 ; freq. x_out nstvout = 500 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 50 ; energies to log file nstenergy = 50 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist = 1.0 ; cut-off distance for the short range neighbour list pbc = xyz ; Periodic boundary conditions:xyz, use periodic boundary conditions in all directions periodic_molecules = no ; molecules are finite, fast molecular pbc can be used coulombtype = PME ; particle-mesh-ewald electrostatics rcoulomb = 1.0 ; distance for the coulomb cut-off vdw-type = Cut-off ; van der Waals interactions rvdw = 1.0 ; distance for the LJ or Buckingham cut-off fourierspacing = 0.12 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order = 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes ; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = v-rescale ; temp. coupling with vel. rescaling with a stochastic term. tau_t = 0.1 ; time constant for coupling tc-grps = OXY ; groups to couple separately to temp. bath ref_t = 80 ; ref. temp. for coupling Pcoupl = berendsen ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p = 0.5 ; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p = 1.0 ; ref. pressure for coupling (bar) gen_vel = yes ; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 80 ; temperature for Maxwell distribution gen_seed = 173529 ; used to initialize random generator for random velocities .mdp file which gave the plot which converges to 1: title = NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 500000 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 500 ; energies to log file nstenergy = 500 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist = 0.3 ; cut-off distance for the short range neighbour list pbc = xyz ; Periodic boundary conditions:xyz, use p b c in all directions periodic_molecules = no ; molecules are finite, fast molecular pbc can be used coulombtype = PME ; particle-mesh-ewald electrostatics rcoulomb = 0.3 ; distance for the coulomb cut-off vdw-type = Cut-off ; van der Waals interactions rvdw = 0.7 ; distance for the LJ or Buckingham cut-off fourierspacing = 0.135 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order = 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes ; calculate optimal FFT plan for the grid at start up. DispCorr = no Tcoupl = nose-hoover; temp. coupling with vel. rescaling with a stochastic term. tau_t = 0.5 ; time constant for coupling tc-grps = OXY ; groups to couple separately to temp. bath ref_t = 80 ; ref. temp. for coupling Pcoupl = parrinello-rahman ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p = 5.0 ; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p = 1.0 ; ref. pressure for coupling (bar) gen_vel = yes ; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 80 ; temperature for Maxwell distribution gen_seed = 173529 ; used to initialize random generator for random velocities I appreciate your reply. Lum
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