[gmx-users] Heat of vap

[Elisabeth]

>
> 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.
>
> Hello David and Justin,

My explanation was not clear. Below is the results for liquid phase and for
gas phase I tried two cases: one single molecule and the other time for
equivalent number of molecules as in liquid phase and thats why results are
very similar. ( However Justin says one single molecule is not correct. I
think when cutoffs is set to zero only bonded terms are treated and even
where there are many particles in gas phase to get energies per mole of
molecules i.e g_energy -nmol XXX must be used so values should be colse to a
single molecules case.. please correct me!  Anyway results for gas phase are
close and this is not the issue now).

Liquid phase:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
LJ (SR)                    -27.3083       0.01   0.296591 -0.0389173
(kJ/mol)
Coulomb (SR)                6.00527     0.0074   0.122878 0.00576827
(kJ/mol)
Coul. recip.                5.59559     0.0032  0.0557413 0.00316957
(kJ/mol)
Potential                   *34.6779  *    0.025    1.03468   -0.11177
(kJ/mol)
Total Energy                86.4044      0.026    1.44353  -0.112587
(kJ/mol)




>  *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.
>
> Thanks Justin. I am interested in the energy required to vaporize the
> solute in a particular solvent not the whole DHvap of the mixture. do you
> think this can be achieved by calculating nonbonded energies between solute
> and solvent? ( defining energy groups ..)
>


>
>> 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.
>
> What you mean is when one uses PME interaction energies between components
> can not be decomposed? So the energy groups I defined to extract nonbonded
> energies are not giving correct values? Sofar I have been defining energy
> groups to calculate nonbonded terms between components _A-A A_B... I hope I
> have not been doing thing wrongly!
>

Please help me out!

Thanks,
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