Anna-Pitschna E. Kunz

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For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some(More)
Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamics (MD) simulation are described: the treatment of electronic polarizability, an implicit surface area and(More)
A method to enhance sampling of rare events is presented. It makes use of distance or dihedral-angle restraints to overcome an energy barrier separating two metastable states or to stabilize a transition state between the two metastable states. In order not to perturb these metastable end states themselves, a prefactor is introduced into the restraining(More)
Methodology to compute the relative static dielectric permittivity and dielectric relaxation time of molecular liquids is reviewed and explicit formulas are given for the external field method in the case of simulations using a spherical cutoff, in which the background dielectric permittivity (εcs) can be larger than one, in combination with a(More)
Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is determined, this(More)
A method to enhance sampling of a small subset of N(h) particular degrees of freedom of a system of N(h) + N(l) degrees of freedom is presented. It makes use of adiabatically decoupling these degrees of freedom by increasing their mass followed by either increasing their temperature or reducing their interaction or the force acting on them. The appropriate(More)
Three methods to enhance the configurational sampling of ions in aqueous solution, temperature and Hamiltonian replica exchange and adiabatic decoupling with translational temperature scaling, were compared for a system of CaSO(4) in water. It took 11 replicas in the case of temperature replica exchange to make use of a diffusion coefficient that is a(More)
A method for conformational Boltzmann sampling of loops in proteins in aqueous solution is presented that is based on adiabatic decoupling molecular dynamics (MD) simulation with temperature or force scaling. To illustrate the enhanced sampling, the loop from residues 33 to 43 in the bovine protein ribonuclease A is adiabatically decoupled from the rest of(More)
A new charge-on-spring (COS) model for water is introduced (COS/D). It includes a sublinear dependence of the induced dipole on the electric field for large field strength to include the effect of hyperpolarizability by damping the polarizability. Only two new parameters were introduced to define the damping of the polarizability. In the parametrization(More)
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