Dear all<br>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:<br>
<br>Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets<br>All averages are exact over 3762001 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
Temperature 298 125.156 125.156 1.9202e-05 0.144476<br>Volume 126.908 53.2917 53.2917 5.61522e-06 0.0422489<br>Density (SI) 972.142 408.201 408.201 -4.30887e-05 -0.324199<br>
Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389)<br>Isothermal Compressibility: 0.543909 /bar<br>Adiabatic bulk modulus: 1.83854 bar<br><br>Why am I obtaining so low density? The density seems to be constant over that timescale.<br>
<br>This is my mdp file:<br><br>constraints = all-bonds <br>integrator = md <br>dt = 0.002 <br>nsteps = 2500000 <br><br>nstxout = 5000 <br>
nstvout = 50000 <br>nstenergy = 1000 <br>nstxtcout = 5000 <br>energygrps = SOL <br>nstlist = 5 <br> <br>ns_type = grid <br>
rlist = 1.2 <br>rcoulomb = 1.2 <br>rvdw = 1.2 <br>coulombtype = PME <br>fourierspacing = 0.15 <br>pme_order = 4 <br>ewald_rtol = 1e-5 <br>
optimize_fft = yes<br><br>Tcoupl = nose-hoover <br>tau_t = 0.1 <br>tc-grps = SOL<br>ref_t = 298 <br><br>Pcoupl = Parrinello-Rahman<br>tau_p = 0.5 <br>
compressibility = 4.5e-5 <br>ref_p = 1.0 <br>pcoupltype = isotropic <br><br>gen_vel = yes<br>gen_temp = 298<br>gen_seed = -1<br><br><br>Thanks in advance for any help...<br>