Dear experts, I am trying to do a MD run for stack of hexane molecules. The density of hexane (Mw 86 g/mol) is about 1 g/cm^3.
Density (g/cm3) Mw hexane (g/mol) NO.molecuels/cm3 NO./nm3 1 86 1/86*6.023E23=7.0E+21 7 using genconf I generated 1000 molecules in 160 nm^3 which gives roughly 1000/160=6 molecuels per nm^3. ( I hope I am doing this calculation properly) 1-I did MD run and below energy values are listed. Please let me know if these figures are reasonable. And more importantly, it would be great if you could introduce some stuff to read so that I am able to interpret the MD results by myself! (especially the energy values). I do not find these info in tutorials and manual. For my hydrocarbon system how I can judge if the results are acceptable or something is wrong in sys. 2- Since I intend to calculate interaction parameters from MD, I think should look more carefully at LJ and coulomb energy terms (non-bonded). Am I right? 3- In md parameter file I set T=300K but in this list I see a little deviation from set value (308K). Why is this happening? I appreciate your help :) Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 29 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 35400.7 5069.14 5039.32 190.167 1902.05 Ryckaert-Bell. 6844.55 678.945 638.128 -80.3023 -803.184 LJ-14 5004.3 457.252 454.848 16.2167 162.2 LJ (SR) -37726 7281.85 5814.25 -1518.38 -15186.8 Coulomb (SR) 5740.07 92.5554 92.4275 1.68437 16.8471 Coul. recip. 7414.94 92.7901 41.726 -28.7044 -287.102 Potential 20192.9 10123.3 9250.53 -1424.19 -14244.7 Kinetic En. 52643 7920.03 7517.68 -863.171 -8633.44 Total Energy 72835.9 16069.4 14649.5 -2287.36 -22878.2 Temperature 308.874 46.4695 44.1088 -5.06452 -50.6553 Pressure (bar) 14682.6 7908.29 6791.02 -1403.56 -14038.4 Cons. rmsd () 3.65871e-06 5.37168e-07 5.36935e-07 5.4798e-09 5.48089e-08 Vir-XX -24979.4 54370 54284.8 1053.98 10541.9 Vir-XY -338.531 30079.9 30079.3 -65.6999 -657.131 Vir-XZ -144.844 1488.44 1482.6 -45.6274 -456.365 Vir-YX -338.531 30079.9 30079.3 -65.6999 -657.131 Vir-YY -73589.4 70663.6 60227.1 12800.7 128033 Vir-YZ -729.092 1475.1 1412.53 147.223 1472.53 Vir-ZX -144.844 1488.44 1482.6 -45.6274 -456.365 Vir-ZY -729.092 1475.1 1412.53 147.223 1472.53 Vir-ZZ -60998.1 18804.5 9754.95 5567.91 55690.2 Pres-XX (bar) 9072.68 11325.2 11306.6 -224.415 -2244.6 Pres-XY (bar) 73.2958 6309.8 6309.07 33.3162 333.229 Pres-XZ (bar) 30.2309 311.054 310.316 7.41674 74.1823 Pres-YX (bar) 73.2958 6309.8 6309.07 33.3162 333.229 Pres-YY (bar) 18908.6 15288.5 13002 -2785.54 -27861 Pres-YZ (bar) 148.517 309.614 295.801 -31.6721 -316.784 Pres-ZX (bar) 30.2309 311.054 310.316 7.41674 74.1823 Pres-ZY (bar) 148.517 309.614 295.801 -31.6721 -316.784 Heat Capacity Cv: 12.9101 J/mol K (factor = 0.0226346)
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