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.
*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.
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.
-Justin
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,
--
========================================
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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