On 2011-04-04 01.32, Justin A. Lemkul wrote:
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.
NOOOOOOOOOOOOOOOOOOOOOO
1 molecule in the gas phase -> Epot(g) in your case 59.2 kJ/mol
N molecules in the liquid phase -> Epot(l) (since this is per mole you
DO need the -nmol option) in you case 34.7 kJ/mol
DHvap = Epot(g) + kBT - Epot(l) = 59.2+2.5-34.7 = 27 kJ/mol which is
quite close to hexane (28.9 kJ/mol).
-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,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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