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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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