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

[Mark Abraham]

On 23/03/11, Elisabeth  <katesedate at gmail.com> wrote:
> 
> 
> On 22 March 2011 22:46, Justin A. Lemkul <jalemkul at vt.edu> wrote:
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> > 
> > 
> > 
> > 
> > 
> > Elisabeth wrote:
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> > 
> > > 
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> > > 
> > > 
> > > 
> > > On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
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> > > 
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> > > 
> > > 
> > >     Elisabeth wrote:
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> > > 
> > > 
> > >         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.! 
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> > 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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