Index

A

Angle Potential

averages

B

Bond Potential bond restraint

born boundary

C

Cartesian restraint chunk combination rules

Coulomb Potential cutoff cuttype

D

debug Deletion Moves design Dihedral Potential

dihedral restraint dlambda dryrun Dual Topology dump files

E

equilibrate

F

fakesime feather fixbackbone

fixresidues Forcefields freeenergy

G

GBSA Potential gcmc

GCSolute Moves GCSolutes grand

H

hardwall restraint

I

Insertion Moves

Intermolecular Potential Intramolecular non-bonded Potential

J

jaws1

jaws2 jbias

L

lambda lambda chunk

lambdaladder lambdare

M

maxvolchange mode angle mode bond mode born mode clj

mode dihedral mode info mode surface mode ureybradley Move Probabilities

O

origin

Output

P

parfile pdb command pdbparam Perturbations potential, [1] prefsampling

pressure prettyprint printfe printmove protein, command Proteins

R

ranseed resetgb Residue Moves

restart command restraints retienergy

S

sameseeds Sample Moves setstream simulate Single Topology singlepoint softcore softcoreparams Solute Moves

solute, command solutenergy Solutes solutetempering solvent chunk Solvent Moves Solvents splitgbsasimulate Streams surface

T

temperature temperatureladder temperaturere

testenergy Theta Moves thres

U

Urey-Bradley Potential

V

van der Waals Potential

Volume Moves