[gmx-users] unit of surface tension, KJ/mol?
Elisabeth
katesedate at gmail.com
Wed Mar 23 05:39:01 CET 2011
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!
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> wrote:
>
>
> On 23/03/11, *Elisabeth * <katesedate at gmail.com> wrote:
>
>
>
> On 22 March 2011 22:46, Justin A. Lemkul <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>> 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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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>
>
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