> > 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 treated and even where there are many particles in gas phase to get 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). 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,
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