![]() If switching is set to off, the van der Waals energy is just abruptly truncated at the cutoff distance, so that energy may not be conserved. A graph of the van der Waals potential with this switching function is shown in Figure 1. With this option set to on,a smooth switching function will be used to truncate thevan der Waals potential energy smoothly at the cutoff distance. The main option that effects van der Waals interactionsis the switching parameter. In NAMD, van der Waals interactions are always truncated at the cutoff distance, specified by cutoff. Van der Waals interactionsThe simplest non-bonded interaction is the van der Waals interaction. These options are interrelated andcan be quite confusing, so this section attempts to explain thebehavior of the non-bonded interactions and how to use theseparameters. ![]() NAMD has a number of options that control the way that non-bondedinteractions are calculated. Next:Water Models Up:Force Field Parameters Previous:Potential energy functions Contents Index Bonded electrons are shared between atoms to create a bond. Lone pairs of electrons are non-bonded electrons. The atoms in polyatomic ions, such as OH –, NO 3−, and NH 4+, are held together by polar covalent bonds. Some compounds contain both covalent and ionic bonds. Bonds between two nonmetals are generally covalent bonding between a metal and a nonmetal is often ionic.
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