CartesianMD

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CartesianMD

CartesianMD calls Molecular Dynamics simulation in Rosetta with user-defined energy function. Runs NVT simulation (constant volume and temperature) with Berendsen thermostat. Integrator uses Velocity Verlet algorithm. Strongly recommended to use the Mover with Rosetta version since February 2016; there was certain issues with the Mover in previous versions.

<CartesianMD name="&string"
       rattle="(true &false)"
       scorefxn="('' &string)"
       scorefxn_obj="('' &string)"
       nstep="(100 &Size)"
       temp="(300.0 &Real)"
       premin="(50 &Size)"
       postmin="(200 &Size)"
       report="(100 &Size)"
       report_scorecomp="(false &bool)"
       selectmode="('final' &string)"
       schfile="('' &string)" />

rattle: Use Rattle algorithm to constraint hydrogen locations. This automatically sets integration step = 2fs. Otherwise uses integration step = 1fs.
scorefxn: Specify a scorefunction to run MD simulation with.
scorefxn_obj: Optional, identical to scorefxn unless specified. Specify a scorefunction to use as objective function for selecting a pose from trajectory. This will be used only when selectmode="minobj".
nstep: Number of steps to simulate. With Rattle on (default) each step is 2fs, and hence, nstep=10000 will be 20ps.
temp: Reference temperature for constant temperature simulation. Recommended values: 150~200K for talaris2014_cart and ~250 for beta_nov15_cart.
premin: Steps of Cartesian minimization before MD simulation
postmin: Steps of Cartesian minimization after MD simulation
report: By how often the mover reports the simulation status to log.
report_scorecomp: Whether to report score components to log.
selectmode: How to select single pose from the trajectory. "final" to take the final pose, "minobj" to take the lowest objective function (by scorefxn_obj) pose.
schfile: Use user-defined schedule file. This overrides any other flags or options. Syntax: "sch [temperature] [nsteps]" to run simulation, or "repack" to repack side-chains. An example schedule file to run simulated annealing:
```
sch 300 10000 
sch 250 10000 
sch 200 10000 
sch 150 10000 
```

This mover can also take an optional MoveMap (see FastRelax documentation for details) to define the residue subset to which it should be applied. In the absence of the MoveMap, the mover is applied to the whole pose.