> Several possible reasons: > > 1. The force field parameters aren't perfect, so there is some inherent > disagreement between simulation and reality. What is the expected value > for > this force field?
> 2. You're using the isothermal compressibility for water. If your system > is > pure liquid benzene, I'd think you would want to use the compressibility > for > benzene. I don't know how big the difference would be off-hand, but at > least > you'd be convinced that your simulation was set up properly. > > 3. Although it won't matter a huge amount, to what temperature does the > experimental density correspond? Usually these parameters are given at 25C > (298 > K). The temperature you've used is 300 K. Again, a minor point, but one > worth > doing correctly in a simulation even though the such a change would not > account > for the magnitude of difference you're currently seeing. > > -Justin > > Hi Justin, Thanks for your suggestions! The OPLSAA model for liquid benzene could get a density of 0.873+/-0.001 g/cm^3 (JACS,1990,112,4768) at 298K and 1 atm. I have done some test and maybe I have found what is the problem. In the previous simulation, I applied long range dispersion corrections for energy and pressure with "DispCorr = EnerPres". When I apply the long range dispersion corrections only for energy with "DispCorr = Ener" (the temperature is set to be 298K and the pressure is set to be 1 bar), the density of the system is 0.883, which is closely to the experimental value and the expect value of this model. Now, I have anther question. After the simulation, I want to calculate the hear capacity of liquid benzene. So I using this command: g_energy -f *.edr -s *.tpr -o energy.xvg -b 10000 -nmol 600 -nconstr 12 And these are the results: Statistics over 5000001 steps [ 10000.0000 through 20000.0000 ps ], 11 data sets All statistics are over 500001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Potential 19.7926 0.036 0.435187 -0.0870648 (kJ/mol) Kinetic En. 29.7264 1.7e-05 0.360236 -7.68964e-05 (kJ/mol) Total Energy 49.519 0.036 0.575006 -0.0871418 (kJ/mol) Temperature 297.999 0.00017 3.61127 -0.000770665 (K) Pressure 1.15978 0.0036 171.048 -0.00963121 (bar) Box-X 4.45033 0.0015 0.0105071 -0.0038387 (nm) Box-Y 4.45033 0.0015 0.0105071 -0.0038387 (nm) Box-Z 4.45033 0.0015 0.0105071 -0.0038387 (nm) Volume 88.1423 0.089 0.624413 -0.228234 (nm^3) Density 883.013 0.89 6.25236 2.28197 (kg/m^3) Enthalpy 29712.2 21 345.005 -52.2857 (kJ/mol) Temperature dependent fluctuation properties at T = 297.999. #constr/mol = 12 Isothermal Compressibility: 0.000107512 /bar Adiabatic bulk modulus: 9301.25 bar Heat capacity at constant pressure Cp: 218.791 J/mol K Thermal expansion coefficient alphaP: 0.000135136 1/K I got a hear capacity at constant pressure with 218.791 J/(mol K). However, the experimental value is 135.98 J/(mol K), and the expect value of the model is 130.54 J/(mol K) (JACS,1990,112,4768). In the new simulation, I used LINCS for all-bonds. So I think the #nconstr should be 12 in the g_energy command. Is this value for #nconstr right? If it is wrong, what value should I use. Or I should not use long range dispersion correction for energy? Are there other mistakes with my parameters? Best regards! Cenfeng Fu
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