Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns:
Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Temperature 298 125.156 125.156 1.9202e-05 0.144476 Volume 126.908 53.2917 53.2917 5.61522e-06 0.0422489 Density (SI) 972.142 408.201 408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus: 1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 2500000 nstxout = 5000 nstvout = 50000 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp = 298 gen_seed = -1 Thanks in advance for any help...
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