[gmx-users] Heat of vap

[David van der Spoel]

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