[gmx-users] Heat of vap
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 3 09:41:43 CEST 2011
On 2011-04-03 02.15, 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:
>
> *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)
This is not correct. You need to simulate the liquid in the liquid
state. Now you have a dilute gas instead, hence the energy difference is
very small and due to dimers and trimers in the gas phase. Just extract
Epot from your previous liquid phase calculations.
>
> 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...!
>
> 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?
>
>
> 1- If I want to look at nonboded interactions only, do I have to add
> Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ?
>
>
> 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,
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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