# Plop command

### From Jacobson Lab Wiki

As of January 26, 2012 this is an exhaustive list of Plop toplevel commands which can be used in a command file.

brownian - Perturbed minimization sampling.

constraint - Setting energetic constraints for bond lengths, angles, dihedrals.

datadirectory - Specify a path to a plop data directory.

domain

dynamics - Molecular dynamics simulations.

energy - Energy commands, such as setting a solvent model.

evaluate

file - Used to set some output file paths.

global

helix - Helix prediction.

hmc - Hybrid Monte-Carlo.

homology - Homology modeling.

jobname - Set a name for the plop job.

leaf_activate

lig

lig_sampling

load - Loading of input files.

log

loop - Loop prediction and related options.

minimize - Minimization commands and options.

modify

multi_mc

out

pele

pele2

pka

prosane

random - Set a random seed for reproducibility of results in commands that make calls to the random number generator.

rigidbody

rigidmc - Rigid body Metropolis Hastings Monte-Carlo.

rmsd - Compute the RMSD of the structure to a reference structure (and align?).

rot

serialmc - Serial Metropolis Hastings Monte-Carlo incorporating sidechain motions, hybrid-Monte-Carlo, and rigid body Monte Carlo moves.

side - Side chain optimization.

sidemc - Metropolis-Hastings Monte-Carlo sampling, incorporating only sidechain moves.

ss

strand

structure

symmetry

tail

tether

update_charges

verbose

write - Writing of output files.

zmin