[gmx-users] Heat of vap
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 4 01:32:47 CEST 2011
Elisabeth wrote:
>
>
>
>
> 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
What is not correct is comparing the potential energy of a liquid system of many
molecules with a "gas phase" of a single molecule. Whether or not that was
something you did still is not entirely clear, but to be very clear, that's what
I was saying is incorrect to do. DHvap is based on conversion of equivalent
systems between liquid and gas.
> treated and even where there are many particles in gas phase to get
This is incorrect. Cutoffs of zero mean that all nonbonded interactions are
calculated, they are not truncated.
> 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).
>
You shouldn't need -nmol for any of this. Simply take the potential energy of
the two systems (with equivalent numbers of molecules) and apply the formula I
gave you several emails ago.
-Justin
> 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,
>
--
========================================
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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