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.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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