[gmx-users] unit of surface tension, KJ/mol?
Elisabeth
katesedate at gmail.com
Wed Mar 23 17:23:24 CET 2011
Thanks for your help. :)
On 23 March 2011 07:47, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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> gmx-users mailing list gmx-users at gromacs.org
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