# [gmx-users] unit of surface tension, KJ/mol?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 23 12:44:09 CET 2011

```On 23/03/2011 3:39 PM, Elisabeth wrote:
> Thanks Mark for the hints. I am using a pre equilibrated box for both
> runs. Can you again explain how Can I interpret this from fluctuations
> from two runs? Below is the resutls from two versions: Thanks!

IIRC the contents of the .edr file didn't change across these versions,
but the reporting of computed quantities did, so I'd make my life
simpler and use only the 4.5.3 g_energy.

Both simulations have a much higher value for the root-mean-squared
deviation from the average (i.e. standard deviation) than for the
average. So that means your data set looks something like "10000 20 6543
200 23444 23434 15 500 3444". Look at the .xvg file that is produced.
You need a heck of a lot of such data to have confidence that your
sample average reflects the true average. If you haven't got that pile
of data, then you haven't observed the average with any confidence. This
is normal for quantities computed from fluctuations in atomic positions.
They're macroscopic quantities, and have to be observed over a lot of
microscopic configurations.

Be sure to check visually that your system is doing what you hope it is
doing.

Mark

>
> 4.0.7
>
> Statistics over 733801 steps [ 0.0000 thru 1467.6001 ps ], 1 data sets
> All averages are exact over 733801 steps
>
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen               203.778    3623.99    3623.98
> -0.00203751   -2.99026
>
>
> Statistics over 483401 steps [ 500.0000 thru 1466.8000 ps ], 1 data sets
> All averages are exact over 483401 steps
>
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen               203.129    3612.58    3612.28
> 0.168686    163.086
> -----------------------------------------------------------------------------------------------------------------
> 4.5.3
>
>
>
> Statistics over 732501 steps [ 1.0000 through 1466.0000 ps ], 1 data sets
> All statistics are over 73251 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen               2374.49        570    21081.3   -3251.38
> (bar nm)
>
> Statistics over 384501 steps [ 1000.0000 through 1769.0000 ps ], 1
> data sets
> All statistics are over 38451 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen               2610.25       1000    21109.9    4638.38
> (bar nm)
>
> Statistics over 483001 steps [ 500.0000 through 1466.0000 ps ], 1 data
> sets
> All statistics are over 48301 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> #Surf*SurfTen               1645.07        390    20288.3   -174.289
> (bar nm)
>
>
>
>
>
> On 22 March 2011 23:56, Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>> wrote:
>
>
>
>     On 23/03/11, *Elisabeth * <katesedate at gmail.com
>     <mailto:katesedate at gmail.com>> wrote:
>>
>>
>>     On 22 March 2011 22:46, Justin A. Lemkul <jalemkul at vt.edu
>>     <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>         Elisabeth wrote:
>>
>>
>>
>>             On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu
>>             <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>             <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>>                Elisabeth wrote:
>>
>>                    Hello,
>>                     I did two simulations on the same system using
>>             versions 4.0.7
>>                    and 4.5.3. It seems like the unit of surface
>>             tension is not the
>>                    same in these versions because I am getting ~250
>>             KJ/mol an in
>>                    4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can
>>             be converted
>>                    into bar nm? Can anyone help please.
>>
>>
>>                Is this from g_energy output?  In past versions,
>>             everything was
>>                printed as "kJ/mol," even quantities that obviously
>>             weren't, like
>>                temperature, pressure, etc.
>>
>>
>>             Yes, so why are the results so different. I am using
>>             exactly the same mdp file.!
>>
>>
>>         Any pressure-related quantity is going to be subject to
>>         enormous fluctuations. This has been discussed within the
>>         last few days.  Without seeing the .mdp file and a
>>         description of the system, it's hard for anyone to comment on
>>         what the results might mean.
>>
>>
>>     Thanks. I am working on a pure alkane system, in a box of 3X3X3
>>     which is extended in Z to create liq/air interface. That is 3X3X6
>>     . What could be reason for such a big difference in results from
>>     two version? Thanks alot!
>
>     Look at the size of the fluctuations printed by g_energy. If
>     they're comparable or larger than your differences, then you are
>     not observing a statistically significant difference. Over just
>     2ns of a small system, that's likely to be the case. Damping such
>     fluctuations requires large simulations or long times or both.
>
>     You are also generating velocities at the start of this run, so
>     probably you are including spurious measurements on
>     non-equilibrated configurations in your statistics. If you'd
>     thought to tell us your command lines, I wouldn't be guessing :-)
>     You can fix this with g_energy -b, but really you should separate
>     really need to, so that all your workflows have similar
>     properties. Then when you come back to repeat some analysis in a
>     month's time, you don't have to remember to ignore the first 1ns
>     of this simulation...
>
>     Mark
>
>
>>     integrator          =  md
>>     dt                  =  0.002
>>     nsteps              =  1000000
>>
>>     nstenergy           =  100
>>     nstxout             =  100
>>     nstlist             =  10
>>     ns_type             =  grid
>>     coulombtype         =  PME
>>     vdw-type            =  Shift
>>     rcoulomb-switch     =  0
>>     rvdw-switch         =  0
>>     rlist               =  1.1
>>     rcoulomb            =  1.1
>>     rvdw                =  1.0
>>
>>     fourierspacing      =  0.12
>>     fourier_nx          =  0
>>     fourier_ny          =  0
>>     fourier_nz          =  0
>>     pme_order          =  4
>>     ewald_rtol          =  1e-5
>>     ;optimize_fft      =  yes
>>
>>     Tcoupl              =  v-rescale
>>     tc-grps             =  System
>>     tau_t               =  0.1
>>     ref_t               =  300
>>
>>     pbc              =  xyz
>>
>>     gen_vel             =  yes
>>     gen_temp            =  300.0
>>     gen_seed            =  173529
>>
>>     constraints             = all-bonds
>>     constraint-algorithm = lincs
>>
>>
>>         -Justin
>>
>>
>>
>>         --
>>         ========================================
>>
>>         Justin A. Lemkul
>>         Ph.D. Candidate
>>         ICTAS Doctoral Scholar
>>         MILES-IGERT Trainee
>>         Department of Biochemistry
>>         Virginia Tech
>>         Blacksburg, VA
>>         jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>         ========================================
>>         --
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