[gmx-users] Heat of vap

Elisabeth katesedate at gmail.com
Sun Apr 3 02:15:32 CEST 2011

```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)

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