# Systems


# xml files

# OpenMM implicit

1PLXImplicit
ala10Implicit
bench10
bench0
bench1
bench2
bench3
bench4
sv582Implicit
bench80
bench81
dnaDickersonImplicit
bptiImplicit
lambdaImplicit
lysoImplicit
bench102
6TNAImplicit
ProteinAmberImplicit
spectrinImplicit
bench101
CheYObc
1notGbviImplicit
CheYGbvi
sv582_sdGbvi
lambda_sdGbvi
bpti_sdGbvi

# OpenMM explicit

ala10Explicit
bptiExplicit
bptiExplicitAngleConstraints
dnaDickersonExplicit
lambdaExplicit
lysoExplicit
sv582Explicit
tna6Explicit
water12AExplicit
lambdaWaterPMEBarostat
bptiExplicitPMEBarostat
bptiExplicitPMEBarostat

# Gromacs comparison

sv582ImplicitSolventGromacs
bptiImplicitSolventGromacs
1plxImplicitSolventGromacs
lambdaImplicitSolventGromacs
tna6ImplicitSolventGromacs
dnaDickersonImplicitSolventGromacs
ala10ImplicitSolventGromacs


# Gromacs 4.5 comparisons
ubiquitinImplicitGromacsCharmm
ubiquitinImplicitGromacsAmber99
ubiquitinImplicitGromacsAmber94
ubiquitinAmber94PMEGromacs
ubiquitinAmber94NoGbsa
ubiquitinAmber94NonPeriodicGromacs
ubiquitinAmber94PeriodicGromacs
ubiquitinAmber99PMEGromacs
ala10ImplicitGromacs
bptiImplicitGromacs
lysoImplicitGromacs
spectrinImplicitGromacs
bench101ImplicitGromacs
ala10ExplicitPMEGromacs
ala10ExplicitNonPeriodicGromacs

# Amoeba CMAPTorsion 

villin_cmap

# Amoeba

villinAmoeba
alatetAmoeba
diala-DAmoeba
diala-LAmoeba
ubiquitinAmoeba
ammoniaAmoeba
argAmoeba

# parameter text files

1plxImplicitSolvent
ala10ImplicitSolvent
bptiGbviImplicitSolvent
bptiImplicitSolvent
dnaDickersonImplicitSolvent
lambdaImplicitSolvent
lysoImplicitSolvent
spectrinImplicitSolvent
sv582ImplicitSolvent
tna6ImplicitSolvent

ala10ExplicitSolvent
ala10ExplicitSolventCutoffPeriodic
ala10ExplicitSolventCutoffNonPeriodic
bptiExplicitSolvent2
bptiExplicitSolvent
bptiExplicitSolventCutoffPeriodic
bptiExplicitSolventCutoffNonPeriodic
dnaDickersonExplicitSolvent
lambdaExplicitSolvent
lysoExplicitSolvent
sv582ExplicitSolvent
tna6ExplicitSolvent