On 14 February 2010 19:10, Daniel Hoegerl <dan...@hoegerl.org> wrote: > Hi everyone, > > I'll immediately start, so: > > I'm trying to calculate the gibbs energy of a molecule, and first found the > class OBMol and it's method "GetEnergy()". I'm creating the OBMol object from > a SMILES string. However, GetEnergy() allways (well, I tried with a lot > molecules) returns 0.0. > > Then I recognized the OBFieldForce class (example used in the obenergy tool) > and I got rather large energy values in kJ/mol for molecules of at most 240 > amu. Finally I built in the energy minimizing step (using the > pFF->ConjugateGradients(10000)), but only the energy values of small > molecules became smaller - the larger molecules stayed at their high positive > energies (i.e. > 1e10). > > So my first question is: what is this energy in a chemical sense - I thought > it to be the "heat of formation", oder the free enthalpy or even the gibbs > energy!?
Molecular mechanics forcefield energies are not derived from thermodynamics. They treat bonds and angles (etc..) as a system of 'springs' (see Cramer or Jensen's Computational Chemistry textbooks for more background). So what's the point? Well, their relative values can be used to determine the most stable conformer for example. I'm not sure whether it's meaningful to compare the FF energy for one molecule to the FF energy for another, though. > And why is OBMol->GetEnergy() always 0.0? I think this value is only non-zero if you are reading the result of a QM calculation (e.g. a Gaussian log file) (we welcome documentation patches!). > Thanks in advance, > > Daniel > > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
