CHARMM Element doc/dynamc.doc 1.1#File: Dynamc, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Dynamics: Description and DiscussionThere are four separate dynamics integrators available in CHARMM:(This discussion does not apply to multi-body dynamics, which has aseparate set of integrators). See *note Mbond:(chmdoc/mbond.doc).Name Keyword ModuleOriginal Verlet ORIG dynamcv.src Leapfrog Verlet LEAP dynamc.src (default)Velocity Verlet VVER dynamvv.src4-D L-F Verlet VER4 dynam4.srcAll methods are based on the Verlet scheme, and when used withoutany special features, provide identical trajectories for shortsimulations. All methods allow SHAKE.The ORIG integrator is a standard 3-step Verlet integratorwith few frills. It allows: Langevin Dynamics (LANG) Thermodynamic Simulation Method (TSM)The LEAP integrator is similar to the ORIG integrator, but doesprovide increased accuracy (esp. for single precision version ofCHARMM). It allows: Langevin dynamics (LANG) (with accurate temperatures printed) Constant Temperature and Pressure (CPT) (based on Berendsen's method) Accurate pressures with SHAKE High frequency correction to the total energy Parallel code Free energy equilibration indicator (deltaF*V) (with PERT) Thermodynamic Simulation Method (TSM)The VVER integrator also provides increase accuracy. It allows: Constant Temperature (NOSE) (Nose-Hoover method) Multiple Time Step (MTS)The VER4 integrator enables the energy embedding technique that entails placing a molecule into a higher spatial dimension [Crippen, G. M. & Havel,T.F. (1990) J.Chem.Inf.Comput.Sci. Vol 30, 222-227]. The possibility of surmounting energy barriers with these added degrees of freedom may lead to lower energy minima. Here, this is accomplished by molecular dynamics in four dimensions. Specifically, another cartesian coordinates was added to the usual X, Y, and Z coordinates in the LEAPfrog VERLet algorithm.In order to generate a dynamics trajectory, all requirementsfor evaluating the energy must be met.See *note Energy:(chmdoc/energy.doc)Needs. * Menu:* Syntax:: Syntax of the dynamics command* Description:: Description of the keywords and options* Recommended:: Recommended input options and values* Discussion:: Running dynamics* Output:: Output from a dynamics run* Trajectory:: Trajectory manipulation and I/O* Merge:: Merging or breaking up trajectory files into different size pieces. Resampling at a largerinterval. Least squares fit to a reference. Recentering, or undoing image operations.* Reorient:: Reorienting a coordinate trajectory* RMSDyn:: Computes the RMS difference between two trajectories* Format:: formatting and unformatting a dynamics trajectory* CVELocity:: Constant velocity dynamics* TMD:: Targeted molecular dynamics* TSALlis:: Molecular dynamics in the Tsallis ensemble* Monitor:(chmdoc/monitor.doc). Monitor dihedral transitions* CPT dynamics:(chmdoc/pressure.doc). CPT dynamics* 4-D dynamics:(chmdoc/fourd.doc). 4-D dynamics* Pressure:(chmdoc/pressure.doc)Pressure. The pressure command* MTS:(chmdoc/mts.doc). Multiple Time Scales Method* Nose:(chmdoc/nose.doc). Nose-Hoover Dynamics* MBOND:(chmdoc/mbond.doc)Dynamic. Multi-body Dynamics#File: Dynamc, Node: Syntax, Up: Top, Previous: Top, Next: Description Syntax for the Dynamics CommandDYNAmics { [ LEAP ] [ VERLet ] } ! Dynamics with the leap-frog integrator { [ NEW ] [ LANGevin ] } { [ CPT ] [ NOLAngevin ] } other-specs cpt-spec { [ EULEr ] } { ORIG } ! Dynamics with the verlet integratorDYNAmics { VVERlet [ NOSE ] } ! Dynamics with the velocity verlet integrator { } other-specsDYNAmics { LEAPfrog VER4 four-dim-spec } ! Four dimensional dynamics { } other-specsDYNAmics { MBONd mbond-spec } other-specs ! Multibody dynamicsother-specs::= [NSTEp integer] [nonbond-spec] [hbond-spec] [frequency-spec] {[TIMEstp real]} {STARt } [unit-spec] [temperature-spec] [options-spec] { AKMA real } {RESTart}hbond-spec::= see *note Hbonds:(chmdoc/hbonds.doc).nonbond-spec::= See *note Nbonds:(chmdoc/nbonds.doc).mbond-spec::= See *note Mbond:(chmdoc/mbond.doc)DynDesc.frequency-spec::= [INBFrq integer] [IEQFrq integer] [IHBFrq integer] [IHTFrq integer] [IPRFrq integer] [NPRInt integer] [NSAVC integer] [NSAVV integer] [NTRFrq integer] [ILBFrq integer] [ISVFRQ integer] [NSAVL integer] [IMGFrq integer] [IXTFrq integer] [NLAT integer] [NBLCkfep integer] unit-spec::= [IUNCrd integer] [IUNRea integer] [IUNVel integer] [IUNWri integer] [KUNIt integer] [CRAShu integer] [BACKup integer] [IUNLdm integer] [ILAT integer] [IBLCkfep integer] [ILAP integer] [ILAF integer] temperature-spec::= [FINAlt real] [FIRStt real] [TEMInc real][TSTRuc real] [TWINDH real] [TWINDL real] [TBATh real]options-spec::= [IASOrs integer] [IASVel integer] [ICHEcw integer] [ISCAle integer] [ISCVel integer] [ISEEd integer] [SCALe real] [NDEGg integer] [RBUFfer real] [AVERage] [ECHEck real] [TOL real]cpt-spec::= See *note cpt:(chmdoc/pressure.doc)four-dim-spec::= [FIL4dimension] [SKBOnd] [SKANgle] [SKDIhedral] [SKVDerWaals] [SKELectrostatics] [K4DInitial real] [INC4Dforce integer] [DEC4Dforce integer] [MULTK4di real] [E4FILLcoordinates real] [FNLT4 real] [FSTT4 real] [TIN4 real] [IHT4 integer] [IEQ4 integer] [ICH4 integer] [TWH4 real] [TWL4 real]#File: Dynamc, Node: Description,