Moeed wrote:
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.
Where are you getting this density? A quick Google search turns up various
sources of information that point to a density on the order of 0.65 g/mL. Crude
approximations, especially in microscopic systems, have huge implications.
Density (g/cm3) Mw hexane (g/mol) NO.molecuels/cm3
NO./nm3
1 86 1/86*6.023E23=7.0E+21 7
If you use the right density, you get about 4.5 molecules/nm^3...
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)
Well, that'd be the right way to calculate how many molecules you need (but
again I think the underlying calculation is wrong). Also question yourself
whether or not you need a system of such large dimensions! You can scale down
if you want, depending on your needs.
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.
Here's a lesson in conducting MD: decide what you need to calculate before
taking the time to do the simulation. What are you trying to prove by doing the
simulation? Are you trying to demonstrate that the density is stable? Radial
distribution function? Some other intramolecular parameters related to hexane?
Simply dumping out terms from the .edr file will do nothing for you unless you
know what you're looking for.
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?
What is an interaction parameter? Is it calculated from LJ and Coulombic terms?
All systems have these interactions, so I don't know what it is you need to be
doing here.
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?
There is no way to know unless you provide us your complete .mdp file. There
are a number of factors therein that will affect temperature.
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
I don't see density listed below. Is this because you didn't print it out, or
you used a constant volume (NVT) ensemble? As I've said before, forcing the
density to fit some preconceived configuration or assembly is meaningless,
unless you are trying to represent some constant volume (i.e. bomb calorimeter)
conditions. The true measure of whether or not your approach is correct is if
you get a reasonable density under NPT (i.e. real life) conditions...
-Justin
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)
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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