CHARMM code

The CHARMM code, version c25bl, was chosen for integration with the metal potential. CHARMM is a multi-purpose molecular dynamics program [35], which uses empirical potential energy functions to simulate a variety of systems, including proteins, nucleic acids, lipids, sugars and water. The availability of periodic boundary conditions of various lattice types (for example cubic and orthorhombic) makes it possible to treat solids as well as liquids. 

Explicit Solvent, 300 K 3658 T1P3 Water PBC 90 X 36 X 36 9-11 A switched cutoff 60 ps heat, equil 80 ps data collection CHARMM code... 

Classified as intermediate -sized codes within the chemistry community (= 100K-200K lines), simulation packages such as CHARMM, Djg. 

LAMMPS. Another message-passing MD code is LAMMPS [33] used for high-performance parallelized molecular dynamics calculations. The current version (version 17) is compatible with both AMBER and CHARMM. 

Charmm PB APBS codes utilized in the CHARMM package. Available http //biowulf.nih.gov/apps/charmm/charmmdoc/c33b2/apbs.html, or FD approach http //biowulf.nih.gov/apps/charmm/charmmdoc/c33b2/ pbeq.html. 

CHARMM, which stands for Chemistry at HARvard Molecular Mechanics, is one of the oldest and most widely used MD codes. It originated... 

In the genetic algorithm, each probe may be mutated to any of 15 CHARMM atom types or to a null atom. - The string of atom types of each probe constitutes the genetic code of one particular receptor model as in Figure 7.202 [(1 the first step, a population of hundreds of models is randomly generated. The GERM probes of a particular model are used to calculate the interac-... 

One of the first codes was CHARMM (the commercial version is called CHARMm), originally developed at Harvard University. This suite of programs is very versatile and contains all major... 

In our lab we are happy with the NAMD code (Phillips et al. 2005). It is well documented, relatively fast, well maintained, frequently updated and scales nicely. It has certain flexibility in selection of the force field (CHARMM, AMBER). The authors have implemented Locally Enhanced Sampling (LES), Implicit Ligand Sampling (ILS), Replica Exchange, and Steered Molecular Dynamics (SMD) schemes. New versions of NAMD will run on a GPU, and there are also some attempts to port this code to a computational grid environment. 

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