Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

Transferability of the coarse-grained potentials for trans-1,4-polybutadiene

The CG torsion potential has a dual effect on the reproduction of crystallization of trans-1,4-polybutadiene in CG simulation.

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cvis only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032Dis an accurate force field that can be used for protein folding simulations.

The Effect of AIREBO on Thermal Conductivity of EPDM Networks

In this article, thermal conductivity of EPDM networks has been discussed using molecular dynamics simulations. The simulations are performed on four systems using adaptive intermolecular reactive empirical bond order (AIREBO) potential. The effect of Lennard-Jones (L-J) potential and torsion potential on thermal conductivity is discussed. The contribution of L-J potential to thermal conductivity is negative. However, contribution of torsion potential is positive. The results suggest that the randomly entanglement of molecular chains in EPDM networks is responsible for its low thermal conductivity.