примеры использования
Our all-atom representation of the protein permits the parameterization of the free-energy landscape on the basis of physical interactions that are well understood for smaller systems.
The parameterization is generally carried out a priori using ab initio calculations on representative molecular clusters, although alternatives are possible.
For the aliphatic linker region, parameterization was straightforward because this region is chemically sufficiently similar to aliphatic groups in the GROMACS force field.
Although it is reasonable to use the same distance criterion as in the parameterization of the statistical contact potentials, we applied all three criteria of Altuvia et al. to enable a direct comparison of the results.
These details may reflect imperfections of the force field, which is not parameterized to account for ligand to metal charge transfer and polarization effects.
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