On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 10/5/15 2:01 PM, Rasoul Nasiri wrote: > >> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 10/5/15 1:50 PM, Pallavi Banerjee wrote: >>> >>> Correct me if I am wrong, please. Ugas would be obtained from a >>>> simulation >>>> of a single molecule in vacuum. And U liq would be the total potential >>>> energy of the system (which is given by g_energy) minus the total bonded >>>> potential energy (bonds+angles+dihedrals). Am I thinking right? >>>> >>>> >>>> No. It's the actual potential energy. You need the whole potential >>> energy to account for flexibility in the molecule. >>> >>> >>> Hopefully FFs can do this because of the anharmonicity effects caused by >> multi-structural effects (e.g., many coupling of torsions). This >> scenario will be serious when T goes up. >> >> > Indeed it depends to some extent on the size, flexibility, and chemical > composition of the molecule. Additive FFs will inherently overestimate > dipole moments to account for a lack of polarization response, so generally > very polar molecules have poor DHvap values with additive models. Simple > hydrophobics are easier and often agree better with experimental data. > It's even complex behaviour for long chain apolar molecules as there are many possibility for taken into account the coupling effects (rot, vib, conf and so on) especially at high T. Rasoul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
