Dear all,
I've been attempting to obtain water density at 1 bar / 353 K utilizing varying barostats and electrostatic methods. None of the runs are giving the desired density (< 1 gr/cm3). In fact the barostat is failing to reach the desired pressure which is 1 bar. It converges to a much higher pressure resulting in higher density values (~ 1 gr/cm3). Here's a summary of MD settings employed.
The sole thing that crossed my mind is perhaps the current system containing 100 water molecules isnt large enough. If you could please make some remarks on the finest MD parameters (barostat).
Much appreciated.
--- Dynamics parameters ----
Ensemble : NPT
Temperature : 353.00 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 : COMPASSIII (Version 1.1)
Charges : Charge using Gasteiger
Electrostatic terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
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
---- Thermostat ----
Nose mass parameter, Q mass: 6.2923 kcal/mol*ps^2
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) -2787.259 -1214.564 -702.418 718.355
Pot. energy (kcal/mol) -3052.749 -1437.734 -1017.125 760.447
Kin. energy (kcal/mol) 265.489 223.170 314.707 108.208
Tot. enthalpy (kcal/mol) -7351.651 23780.755 -698.327 32832.868
Temperature (K) 297.881 250.398 353.103 121.410
Pressure (GPa) -10.601 61.749 5.252 78.132
Volume (A^3) 2991.461 2812.344 2954.729 199.176
Density (g/cm^3) 1.000 1.064 1.017 0.069
-----------------------------------------------------------------=========================================================
--- Dynamics parameters ----
Ensemble : NPT
Temperature : 353.00 K
Control method : Berendsen
Decay constant : 0.1000000 ps
Pressure : 0.0001 GPa
Control method : Parrinello
Cell time constant : 1.0000000 ps
Timestep : 0.50 fs
Number of steps : 2000000
Duration : 1000 ps
Initial velocities : From structure
---- Energy parameters ----
Forcefield : COMPASSIII (Version 1.1)
Charges : Charge using Gasteiger
Electrostatic terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
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
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) -2787.259 -2792.629 -2757.114 18.138
Pot. energy (kcal/mol) -3052.749 -3121.859 -3071.732 21.103
Kin. energy (kcal/mol) 265.489 329.230 314.617 10.737
Tot. enthalpy (kcal/mol) -7351.651 -3033.631 -2757.073 981.680
Temperature (K) 297.881 369.398 353.002 12.047
Pressure (GPa) -10.601 -0.570 0.002 2.314
Volume (A^3) 2991.461 2936.888 2947.277 8.234
Density (g/cm^3) 1.000 1.019 1.015 0.003
======================================================================
nsemble : NPT
Temperature : 353.00 K
Control method : Berendsen
Decay constant : 0.1000000 ps
Pressure : 0.0001 GPa
Control method : Parrinello
Cell time constant : 1.0000000 ps
Timestep : 0.50 fs
Number of steps : 2000000
Duration : 1000 ps
Initial velocities : From structure
---- Energy parameters ----
Forcefield : COMPASSIII (Version 1.1)
Charges : Forcefield assigned
Electrostatic terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
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
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) -12758.154 -13889.859 -13888.570 14.398
Pot. energy (kcal/mol) -13023.643 -14197.684 -14203.365 13.527
Kin. energy (kcal/mol) 265.489 307.825 314.795 12.368
Tot. enthalpy (kcal/mol) -29608.940 -18218.408 -13888.534 2048.013
Temperature (K) 297.881 345.382 353.201 13.877
Pressure (GPa) -39.136 -10.124 0.002 4.793
Volume (A^3) 2991.461 2970.609 2968.640 1.334
Density (g/cm^3) 1.000 1.007 1.008 0.000
At this point I assumed the 1 ns run isnt long enough to reach the target P and density. So I ran a 5 ns one with the same settings:
==========================================================================================
5 ns run:
Ensemble : NPT
Temperature : 353.00 K
Control method : Berendsen
Decay constant : 0.1000000 ps
Pressure : 0.0001 GPa
Control method : Parrinello
Cell time constant : 1.0000000 ps
Timestep : 0.50 fs
Number of steps : 10000000
Duration : 5000 ps
Initial velocities : From structure
---- Energy parameters ----
Forcefield : COMPASSIII (Version 1.1)
Charges : Forcefield assigned
Electrostatic terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
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
---- Dynamics summary ----
Initial Final Average Std. Dev.
------- ----- ------- ---------
Tot. energy (kcal/mol) -12758.154 -13889.254 -13889.147 6.571
Pot. energy (kcal/mol) -13023.643 -14201.297 -14203.812 11.366
Kin. energy (kcal/mol) 265.489 312.043 314.665 10.968
Tot. enthalpy (kcal/mol) -29608.940 -13733.924 -13889.105 2048.672
Temperature (K) 297.881 350.114 353.056 12.306
Pressure (GPa) -39.136 0.364 0.002 4.795
Volume (A^3) 2991.461 2967.901 2968.639 1.330
Density (g/cm^3) 1.000 1.008 1.008 0.000
