Dear all,
I'm attempting to obtain the water density at 1 bar. To do so I ran NVT:
---- Dynamics parameters ----
Ensemble : NVT
Temperature : 298.00 K
Control method : Nose
Q ratio : 0.0100000
Timestep : 1.00 fs
Number of steps : 5000
Duration : 5 ps
Initial velocities : Random
Random number seed : 1643007721
---- Energy parameters ----
Forcefield : Dreiding
Charges : Use current
Electrostatic terms:
Summation method : Ewald
Accuracy : 0.0001 kcal/mol
Buffer width : 0.5 A
van der Waals terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
Long range correction : YES
Buffer width : 0.5 A
Hydrogen bond terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 4.5 A
Spline width : 0.5 A
Buffer width : 0.5 A
---- Thermostat ----
Nose mass parameter, Q mass: 5.31192 kcal/mol*ps^2
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) 142.076 125.610 128.099 13.744
Pot. energy (kcal/mol) -123.520 -128.922 -137.246 10.848
Kin. energy (kcal/mol) 265.596 254.533 265.345 12.669
Tot. enthalpy (kcal/mol) -294.369 456.478 373.975 116.041
Temperature (K) 298.000 285.587 297.719 14.215
Pressure (GPa) -1.014 0.768 0.571 0.269
Volume (A^3) 2991.461 2991.461 2991.461 0.000
Density (g/cm^3) 1.000 1.000 1.000 0.000
Followed by a NPT:
--- Dynamics parameters ----
Ensemble : NPT
Temperature : 298.00 K
Control method : Nose
Q ratio : 0.0100000
Pressure : 0.0001 GPa
Control method : Berendsen
Decay constant : 0.1000000 ps
Timestep : 0.50 fs
Number of steps : 2000000
Duration : 1000 ps
Initial velocities : From structure
---- Energy parameters ----
Forcefield : Dreiding
Charges : Use current
Electrostatic terms:
Summation method : Ewald
Accuracy : 0.0001 kcal/mol
Buffer width : 0.5 A
van der Waals terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
Long range correction : YES
Buffer width : 0.5 A
Hydrogen bond terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 4.5 A
Spline width : 0.5 A
Buffer width : 0.5 A
---- Thermostat ----
Nose mass parameter, Q mass: 5.31192 kcal/mol*ps^2
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) 142.076 326.376 339.441 18.485
Pot. energy (kcal/mol) -123.520 70.248 73.845 14.757
Kin. energy (kcal/mol) 265.596 256.128 265.596 11.339
Tot. enthalpy (kcal/mol) -294.369 335.582 397.130 57.768
Temperature (K) 298.000 287.377 298.000 12.723
Pressure (GPa) -1.014 0.000 0.002 0.007
Volume (A^3) 2991.461 1184487.771 598989.792 347779.282
Density (g/cm^3) 1.000 0.003 0.016 0.050
In the case of NPT I picked 0.0001 GPa (= 1atm), nonetheless the simulation cell is growing in size giving a density of neanrly zero at the end of 1 ns run. The expected density is 1 g/cm3 at 1 atm. Please take a look at the attached density as well as cell dimesion profiles.
Could you give some comments on the finest and optimum parameters/settings for these runs?
Much appreciated.
Serene
