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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 23 12:47:38 CET 2011

```
Mark Abraham wrote:
>   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.
>

Actually, 4.5.3 may have the bug:

http://redmine.gromacs.org/issues/696

The quantities in the .edr file are correct, but the output from g_energy is
nonsense.  It was fixed for 4.5.4.

-Justin

> 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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>>>
>>
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>>
>>
>

--
========================================

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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