Discover force field

Stouch. Based on the Discover force field, Stouch et al. created a lipid force field. It was used in several diffusion studies of DPPC, and of small solutes in a DPPC bilayer, and tested with crystal simulations. A recent test on a crystal using NPT boundary conditions gave good agreement with experimental data. ... 

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

This situation changed drastically when it was discovered in the 1990s that density functional (DF) methods do a much better job of modeling force fields than (affordable) wave function based methods. Already within the local density approximation (LDA) of DF theory, vibrational frequencies were predicted with... 

Energies of the complex, the protein, and CDNB were calculated using the CFF91 force field of the Discover and have units of kcal/mol. 

A related issue is how accurately certain quantities must be calculated. It is almost pointless to ask a dynamicist, for example, what is an acceptable uncertainty in a calculation of computed points for a potential energy surface. He/she will answer with some unrealistically small value (and then go off and fit the points with an RMS accuracy of about 2 kcal/mol). Similarly, most experimentalists will answer as accurately as you can" when asked how accurately they need some quantity. The best way of discovering how accurately a number is needed is to understand as much as possible of what is being done experimentally (or theoretically, by dynamidsts). It may be that simply establishing the sign of a few quantities, or their order of magnitude, may be all that is needed to allow experimental results to be consistently and successfully analyzed, as Pulay has pointed out in the context of computing molecular force fields [119]. 

Working on a planet in another galaxy, where laboratory temperatures are 200 K, a scientist discovers a new force field selective for isotopes whose separation promises to fuel a bomb to blow an adjacent planet to smithereens. The maximum force exerted by this field on the two isotopes is 5.00 x 1010 dyn/mol. What is the lowest plate height the scientist can hope to achieve in an Sc-class separation In this field the velocity difference is 2% of the mean (which is remarkably selective for isotopes). What length separation tube is needed to separate the isotopes at unit resolution (Remember, lofty goals are worth the trouble.)... 

Some formulations of the potential energy function (e.g., References 27 and 79, and AMBER, CHARMM, and DISCOVER, as well as most force fields used in small-molecule studies) include terms that allow for bond stretching and bond angle bending, that is, for flexible geometry. Hence, the terms in Eq. [1] are augmented by the expression27... 

However, the studies on the calcium channel blockers remained centered even today around the l,4-dihydropyridine class. Since this class of compounds can also act as calcium channel activators, attention has always been drawn towards their structure-activity relationship studies. Attempts were made to differentiate in the mechanisms of their agonist and antagonist activities. On the basis of the force field and quantum mechanical calculations, Holtze and Marrer [51] discovered a imique area of the molecular potentials where Ca agonists and antagonists possess potential of opposite sign. These authors demonstrated that the molecular potential of a simple receptor site was reduced by interaction with calciiun channel activators and, on the contrary, increased by interaction with calcium channel blockers. These opposite effects probably could be the basis for the opposite actions of DHP enantiomers at the potential-dependent calcium channel. 

The X-ray structures of quartz and calcite were obtained from the FIZ Karlsruhe ICSD database [76]. The chosen model structures were constructed in MATERIALS STUDIO [77] under periodic boundary conditions and were then energy-minimized using the program DISCOVER with COMPASS force field until a maximum derivative better than 0.01 kcal mor A was achieved. 

Fa. Accelrys, Materials Studio with DISCOVER 3.01 and COMPASS - force field version 3.0. 

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