Hello all, I am simulating liquid benzene. Initially, I generate a cubic box with 600 benzene molecules in it. The length of the box is 4.6 nm. Then I do the energy minimization and a NPT simulation for 20 ns. The force field I used for benzene is OPLSAA (JACS,1990,112,4768). And here is my .mdp file for the NPT simulation.
title = benz cpp = /usr/bin/cpp define = integrator = md dt = 0.002 ; ps ! nsteps = 10000000 comm_mode = Linear comm_grps = System nstxout = 0 nstvout = 2500 nstlog = 500 nstenergy = 50 nstxtcout = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = nose-hoover ref_t = 300 tau_t = 0.5 tc_grps = System pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 175298 constraints = hbonds constraint_algorithm = LINCS ;shake_tol = 0.0001 lincs_order = 4 lincs_iter = 1 To my surprise, the density of the system is too large to the experimental value (0.874 g/cm^3). Here are some results from the g_energy command. Statistics over 7500001 steps [ 5000.0000 through 20000.0000 ps ], 8 data sets All statistics are over 750001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 13996.9 15 302.701 -83.3695 (kJ/mol) Temperature 299.976 0.00021 3.38239 -0.000582958 (K) Pressure 1.08499 0.0072 1812.66 -0.026224 (bar) Box-X 4.33432 0.00086 0.0102765 -0.00488475 (nm) Box-Y 4.33432 0.00086 0.0102765 -0.00488475 (nm) Box-Z 4.33432 0.00086 0.0102765 -0.00488475 (nm) Volume 81.4276 0.049 0.579125 -0.275291 (nm^3) Density 955.828 0.57 6.80024 3.23201 (kg/m^3) Why the density is so large ? Could anyone give me some suggestions? Thank you in advance! Sincerely Cenfeng Fu
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