mdlab

GLOSSARY

• .DCD FILES: File used to view an MD simulation or other trajectory generated by CHARMM.
• .PDB FILE: Protein Databank File that contains coordinates and bond information of a molecule or system.
• ABSOLUTE REFERENCES: File or directory path that originates at the root directory of the Linux system.
• ADOPTED-BASIS NEWTON-RAPHSON (ABNR): A derivative method of minimization best suited for large systems.
• CHARMM: A molecular simulation program developed by Chemistry at HARvard Macromolecular Mechanics.
• CLIPPING PLANE TOOL: A VMD tool used to view cross-sections of molecules of interest.
• COMPARISON SET: A coordinate set used to compare differences, apply constraints, and more to a system of interest.
• CONDITIONAL STATEMENTS: Used to execute portions of a script based on user-defined criteria.
• CONJUGATE GRADIENT (CONJ): A minimization procedure somewhat more optimized and calculation-intensive than SD.
• CONSTRAINT FORCE: The force required to keep a reactant at a specific point in a reaction coordinate.
• CONSTRAINTS: Energy terms that apply a restoring force, allowing one to confine a selection to certain coordinates.
• ENERGY MINIMIZATION: A set of procedures that changes atom coordinates to find local minima.
• **FATAL **: A CHARMM error that forces the stream file to exit prematurely.
• FORTRAN LOGICAL UNIT NUMBER: A temporary read/write space used by CHARMM when executing stream files.
• FREE-ENERGY PERTURBATION: A method for measuring the F.E. difference (often ΔG) as a molecule changes one state to another.
• HOMOLOGY MODELING: A modeling method used to construct a protein from a sequence differing slightly from a template.
• INFLUENZA A M2 CHANNEL: A tetrameric, proton-selective channel protein that is essential to viral replication.
• INSERT MODE: A mode used in Linux Vi to add, remove, and edit text. Accessed by pressing i in Vi.
• LOG FILE: A log file shows the results of the CHARMM or NAMD simulation file and is essential for troubleshooting.
• LOOP: A loop is a portion of a script which repeats according to user-specified conditions.
• MOLECULAR DYNAMICS: Simulations that contain a dynamic component which varies over time; e.g. heat, pressure, etc.
• ORTHOGRAPHIC MODE: A VMD display mode which removes persective and portrays objects using constant dimensions.
• PATCH: A CHARMM feature that allows for the PSF of a segment to be manipulated.
• PDB ID: A unique identification code given to every molecular structure on the RCSB Protein Databank.
• PERIODIC BOUNDARIES: Takes a region of a system and creates copies of itself around it. Most useful for molecules in solvent.
• PERSPECTIVE MODE: A VMD display mode which portrays objects with dimensions that vary with distance from the viewer.
• PRINCIPLE STRUCTURE FILE (PSF): Contains important bonding information for the structure of segments in CHARMM.
• RCSB PROTEIN DATABANK: A commonly used online repository of 3D structures such as proteins, nucleic acids, etc.
• RELATIVE REFERENCES: Linux paths that originate in the directory of command execution.
• RENDER: A VMD command which creates a bitmap snapshot of the OpenGL scene window.
• REPRESENTATION: User-defined display properties given to a selection of atoms in VMD.
• RESIDUE TOPOLOGY FILE (RTF): A file which defines the type, mass, and charge of atoms in each reside, allowing for PSF generation.
• RESTART FILES: MD output files that contain information for continuing a trajectory.
• RMSD: Root-mean-square deviation, often used in simulations to determine the difference between structures or conformations or to restrain atoms.
• SELECTION: A CHARMM procedure for applying calculations, changes, etc. to specific atoms in a system.
• SLURM: A Linux scheduling system used for submitting multiple jobs to CHARMM on Marylou and Wolf.
• STEEPEST DECENT (SD): A minimization procedure that locates the nearest local energy minimum for a structure.
• STEREO VISION: A VMD display mode which overlaps two images of an object, creating an illusion of a 3D shape.
• STREAM FILE: An input file (usually with the extension .str) which, when executed, submits input to CHARMM.
• TSM: A CHARMM procedure that facilitates the conversion of one molecule to another in free-energy perturbation.
• UMBRELLA POTENTIAL: A constraint used in umbrella sampling procedures for determining binding energy between molecules.
• VARIABLE: A character string which is assigned a user-determined value and reusable.
• VMD: 3D Molecular visualization software used for analyzing biomolecular systems.
• WILDCARD: A character with specific interpretations in the Unix shell. Includes characters such as ?, *, ~, etc.

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