# [gmx-users] How to interpret MD results

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 20:41:20 CEST 2010

```
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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