Plop command

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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

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