GRID molecular environment

From the terms on the right-hand side of (5.425), it can be seen that residual mixture-fraction fluctuations are produced by spatial gradients in the filtered mixture fraction, and are destroyed by molecular dissipation at sub-grid scales. The multi-environment LES... 

The procedure is called MetaSite (Site of Metabolism prediction) [25]. The MetaSite procedure is fully automated and does not require any user assistance. All the work can be handled and submitted in a batch queue. The molecular interaction fields for CYPs obtained from the GRID package are precomputed and stored inside the software. The semiempirical calculations, phaimacophoric recognition, descriptor handling, similarity computation, and reactivity computation are carried out automatically once the structures of the compounds are provided. The complete calculation is performed in a few seconds in IRIX SGI machines, and is even faster in the Linux or Windows environment. For example, processing a database of 100 compounds, starting from 3D molecular structures, takes about three minutes at full resolution with a... 

The Molecular Lipophilicity Potential (MLP) describes the combined lipophilic effect of all fragments in a molecule on its environment and can be calculated at any point in space around the molecule [Audry, Dubost et al., 1986, 1992 Fauchere, Quarendon et al, 1988 Furet, Sele et al., 1988 Audry, Dallet et al., 1989]. It is defined by considering a molecule surrounded by nonpolar or low polarity organic solvent molecules, and assuming that the solvent molecule distribution around the considered molecule depends on the fragmental or atomic contributions to log P and the distances at which the solvent molecules are from the target molecule. Therefore, the molecular lipophilicity potential at each feth grid point is calculated as... 

Grid Searching - Probing Inter-molecular Interactions at Surfaces and Environments... 

In our lab we are happy with the NAMD code (Phillips et al. 2005). It is well documented, relatively fast, well maintained, frequently updated and scales nicely. It has certain flexibility in selection of the force field (CHARMM, AMBER). The authors have implemented Locally Enhanced Sampling (LES), Implicit Ligand Sampling (ILS), Replica Exchange, and Steered Molecular Dynamics (SMD) schemes. New versions of NAMD will run on a GPU, and there are also some attempts to port this code to a computational grid environment. 

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