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

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Xplor-NIH 2024-09-13