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calculation of () Radial distribution function for the Lennard-Jones model fluid at =, =.. In statistical mechanics, the radial distribution function, (or pair correlation function) () in a system of particles (atoms, molecules, colloids, etc.), describes how density varies as a function of distance from a reference particle.
Lemkul et al. have used steered molecular dynamics simulations to calculate the potential of mean force to assess the stability of Alzheimer's amyloid protofibrils. [6] Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the ...
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. [1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software , distributed under the terms of the GNU General Public License .
Although they differ in how they compute or apply the constraints themselves, the constraints are still modelled using Lagrange multipliers which are computed using the Gauss–Seidel method. The original SHAKE algorithm is capable of constraining both rigid and flexible molecules (eg. water, benzene and biphenyl ) and introduces negligible ...
The forces acting between atoms can be obtained by differentiation of the total energy with respect to atom positions. That is, to get the force on atom one should take the three-dimensional derivative (gradient) of the potential with respect to the position of atom :
A powerful and efficient algorithm is the so-called shooting move. [1] Consider the case of a classical many-body system described by coordinates r and momenta p. Molecular dynamics generates a path as a set of (r t, p t) at discrete times t in [0,T] where T is the length of the path. For a transition from A to B, (r 0, p 0) is in A, and (r T ...
The FEP method was introduced by Robert W. Zwanzig in 1954. [1] According to the free-energy perturbation method, the free-energy difference for going from state A to state B is obtained from the following equation, known as the Zwanzig equation :
All-atom models and simulation inputs for bulk materials and interfaces can be built using Materials Studio, [2] VMD, LAMMPS, CHARMM-GUI, as well as other editing programs. [14] Simulations and analysis can be carried out using many molecular dynamics programs such as Discover, Forcite, LAMMPS , NAMD , GROMACS , and CHARMM .