[gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:
> Dear David,
> 
> I followed your instructions and calculated Heat of vaporization of my 
> alkane once with one molecule in gas phase (no cutoff) and once with 
> equivalent number of molecules as in liquid phase as Justin suggested. 
> Results are as follows:
> 

To get heat of vaporization, you shouldn't be simulating just a single molecule 
in the gas phase, it should be an equivalent number of molecules as you have in 
the liquid phase.

> *one single molecule in gas phase*
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> LJ (SR)                    -2.24473      0.073      1.292   0.342696  
> (kJ/mol)
> Coulomb (SR)                11.5723       0.55    2.17577   -2.33224  
> (kJ/mol)
> Potential                  *  59.244 *      0.94    10.9756    6.35631  
> (kJ/mol)
> Total Energy                106.647          1    15.4828    6.78792  
> (kJ/mol)
> 
> *equivalent number of molecules as in liquid* ( large box 20 nm)
> 
> Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 4 data sets
> All statistics are over 100001 points
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> LJ (SR)                    -2.16367      0.053   0.171542   0.374027  
> (kJ/mol)
> Coulomb (SR)                11.2894       0.23    0.49105   -1.44437  
> (kJ/mol)
> Potential                 *  63.2369    *    1.1    2.47211    7.69756  
> (kJ/mol)
> Total Energy                114.337        1.1    2.65547    7.72258  
> (kJ/mol)
> 
> 
>  Since pbc is set to NO molecules leave the box and I dont know if this 
> all right. I hope the difference is acceptable...!
> 

For "pbc = no" there is no box.

> 0- I am going to do the same calculation but for some polymers solvated 
> in the alkane. For binary system do I need to look at nonboded terms? 
> and then run a simulation for a single polymer in vacuum?
> 
> Can you please provide me with a recipe for Delta Hvap of the solute in 
> a solvent?
> 

The method for calculating heat of vaporization is not dependent upon the 
contents of the system; it is a fundamental thermodynamic definition.  Heat of 
vaporization is not something that can be calculated from a solute in a solvent. 
  You can calculate DHvap for a particular system, but not some subset of that 
system.

> 
> 1- If I want to look at nonboded interactions only, do I have to add  
> Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?
> 
> 

The PME-related terms contain both solute-solvent, solvent-solvent, and 
potentially solute-solute terms (depending on the size and nature of the 
solute), so trying to interpret this term in some pairwise fashion is an 
exercise in futility.

-Justin

> coulombtype         =  PME                      
> vdw-type            =  Shift               
> rcoulomb-switch     =  0                  
> rvdw-switch         =  0.9
> rlist               =  1.2               
> rcoulomb            =  1.2            
> rvdw                =  1.0       
> 
> 
> ff: OPLSAA
> 
> 
> Appreciate your help,
> Best,
> 

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

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

========================================