[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
>> your equilibration from your production run, even if you don't
>> 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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