[gmx-users] How to interpret MD results

[Moeed]

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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