Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Molecular self-assembly is the spontaneous association of molecules under equilibrium
conditions into stable, structurally well-defined aggregates joined by noncovalent bonds …

New protein parameters are reported for the all-atom empirical energy function in the
CHARMM program. The parameter evaluation was based on a self-consistent approach …

We present the derivation of a new molecular mechanical force field for simulating the
structures, conformational energies, and interaction energies of proteins, nucleic acids, and …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Abstract The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg
and Swendsen's Multiple Histogram Technique, has been applied for the first time on …

CHARMM is an academic research program used widely for macromolecular mechanics
and dynamics with versatile analysis and manipulation tools of atomic coordinates and …

I. An Overview of Different Approaches to Studying Chemistry in Solution This paper is a
report on the state of the art and on the perspectives of the theoretical treatments of solvent …

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-
dimensional structures of biological macromolecules, with special emphasis on nuclear …

Molecular dynamics simulations are important tools for understanding the physical basis of
the structure and function of biological macromolecules. The early view of proteins as …