rm optional args for examples

UCL-CCS · Aug 8, 2022 · a684530 · a684530
1 parent 9f0363b
commit a684530
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diff --git a/TIES_MD/examples/ethane/zero_sum/leg1/TIES.cfg b/TIES_MD/examples/ethane/zero_sum/leg1/TIES.cfg
@@ -46,11 +46,6 @@ constraint_column = na
 #AMBER only supported input.
 input_type = AMBER
 
-#If cell basis vectors are given then below options are ignored
-#What type of simulation cell is used valid options are cube, truncatedOctahedron, rhombicDodecahedron or na for manual.
-box_type = na
-edge_length = na
-
 #simulation cell
 cell_basis_vec1 = 34.55,  0.0,  0.0
 cell_basis_vec2 = -11.516722937414105,  32.574214501232206,  0.0

diff --git a/TIES_MD/examples/ethane_namd/zero_sum/leg1/TIES.cfg b/TIES_MD/examples/ethane_namd/zero_sum/leg1/TIES.cfg
@@ -46,9 +46,6 @@ constraint_column = beta_factor
 #What input type is provided, only AMBER supported.
 input_type = AMBER
 
-#What type of simulation cell is used valid options are cube, truncatedOctahedron, rhombicDodecahedron or na for manual.
-box_type = na
-
 #If box_type is na the manually specify box vectors of this simulation, unit Angstrom.
 cell_basis_vec1 = 34.550, 0.0, 0.0
 cell_basis_vec2 = -11.516722937414106, 32.574214501232204, 0.0

diff --git a/TIES_MD/examples/hydration/l1-l2/leg1/TIES.cfg b/TIES_MD/examples/hydration/l1-l2/leg1/TIES.cfg
@@ -46,9 +46,6 @@ constraint_column = beta_factor
 #What input type is provided, only AMBER supported.
 input_type = AMBER
 
-#What type of simulation cell is used valid options are cube, truncatedOctahedron, rhombicDodecahedron or na for manual.
-box_type = na
-
 #If box_type is na the manually specify box vectors of this simulation, unit Angstrom.
 cell_basis_vec1 = 46.644591, 0.0, 0.0
 cell_basis_vec2 = 0.0, 46.888166, 0.0

diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/TIES.cfg b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/TIES.cfg
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.crd b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.crd
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.pdb b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.pdb
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.prmtop b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex.prmtop
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex_nofep.pdb b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/complex_nofep.pdb
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/cons.pdb b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/cons.pdb
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/generate_top.log b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/generate_top.log
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/hybrid.frcmod b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/hybrid.frcmod
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/hybrid.mol2 b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/hybrid.mol2
diff --git a/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/leap.in b/TIES_MD/examples/ligand_protein/ties-l2-l1/com/build/leap.in