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

After the dynamics internal statement has been processed, the variables $DINT_TIME and $DINT_STEPS are set, as appropriate.