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##

Syntax of the
Dynamics Internal Statement

The dynamics internal statement sets up parameters for molecular dynamics in internal coordinates. The GROUp statement is used to explicitly groups rigid regions, while the FIX statement fixes the specified selection in space. The HINGe statement explicitly specifies the internal coordinates for a specific group. After these statements are called, one can use the AUTO TORSion statement to configure all remaining degrees of freedom appropriately for torsion-angle dynamics. The timestep for dynamics can be set to automatically adjust to take advantage of the longer timesteps possible with the internal coordinate dynamics.

**DYNAmics INTErnal****{ dynamics-internal-statement } END**is invoked from the main level of X-PLOR.**dynamics-internal-statement :==**-
**CSELect=selection**- specify coordinates to write to trajectory
file.
**DEPRed=real**- predicted drop in energy in minimization.
**BREAk=sel sel**- specification of bonds to break.
**CBREak=sel sel**- Bonds to break and constrain as being fixed.
**ENDTime=real**- Time duration for integration (in picoseconds).
**ETOLerance=real**- Energy tolerance for auto-stepsize adjust and min.
**GTOLerance=real**- Gradient tolerance for minimization.
**CTOLerance=real**- Tolerance for bond constraints.
**CLOOp=logical**- Use loop constraints (default: FALSE)
**MAXEnergy=real**- Max energy error before stepsize halving.
**MAXTimestep=real**- Max factor for timestep increase (default: 1.025).
**MAXCalls=integer**- Max number of energy evaluations in minimization.
**RESPonse time=real**- response time in multiples of the timestep.
**NPRInt=integer**- How often to print energy information.
**NSAVC=integer**- How often to save coordinates to trajectory file.
**NSAVV=integer**- How often to save velocities to a trajectory file.
**NSTEp=integer**- Number of dynamics steps to take.
**NTRFeq=integer**- How often to reset CM(center of mass), velocity/AM (angular momentum) to zero, in units of step number.
**RESEt**- reset all topology information.
**REUSe=logical**- Reuse topology and trajectory information.
**TRAJectory=file**- Name of coordinate trajectory file.
**VELocity-file=file**- Name of velocity trajectory file.
**SCALe vel=logical**- Use velocity scaling (default: TRUE)
**ADJUst TS=logical**- Use auto-timestep adjustment (default: TRUE).
**TIMEstep=real**- Initial size of dynamics timestep.
**TBATh=real**- Bath temperature.
**FRICtion=real**- Friction coefficient. Don't use with velocity rescaling.
**AUTO TORSion**- Auto hinge/node setup for torsion angles.
**FIX=sel**- Fix specified atoms in space.
**GROUp=sel**- Group specified atoms into node.
**HINGe=type sel**- specify selected atoms given hinge
type. Possible types:
**full**- node translates and rotates freely.
**rotate**- node rotates freely - no translation.
**translate**- node translates freely - no rotation.
**torsion**- allow rotation of child hinge about bond connecting it to its parent.
**bend**- allow only bending motion. When using this hinge type, sel should specify only a single atom, and two additonal selections are required. The second selection should specify the parent atom, and the third should define the bend angle.
**bendtorsion**- in addition to torsion motion, allow bending. Requirements for the atom selection are the same as for bend hinges.

**ITYPe=type**- integrator (or minimizer) selection
(default: PC6). The Powell method (Powell, 1977)
is suggested for
minimization.
Possible values:
**PC6**- 6th order predictor-corrector integration.
**Gear**- Gear predictor-corrector integration.
**Milne**- Milne predictor-corrector integration.
**RungeKutta**- Runge-Kutta integration.
**Verlet**- Velocity Verlet integration.
**MinimizeCG**- conjugate-gradient minimization with gradient test.
**Powell**- Powell's method conjugate gradient minimization.
**ConMin**- Simple conjugate-gradient minimization.
**Simplex**- Simplex method for integration.

**PRINt=spec**- print internal information about topology,
integration or minimization quantities. Spec can be one of
**GROUp**- print atoms in each specified group
**HINGe**- print user-defined hinge types
**NODE**- print contents and type of each node
**VERBose=vspec**- print verbose data, where vspec is one of
**reset****coords****resetcm****velfromcartcost****energy****temperature****cmvel****nodeforce****nodepos****nodetheta****nodedef****stepinfo****stepdebug****loopinfo****loopdebug**

*Xplor-NIH 2024-09-13*