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sample.map
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sample.map
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# pdb, gro, dcd, xtc, lammptrj are supported.
AATRAJ = AA_traj.xtc # atomistic trajcetory path
CGTRAJ = CG_traj.lammpstrj # CG trajcetory path
MOL = PRP PRPO # The names of all types of molecules in the system (Propane , 1-Propanol)
NMOL = 100 150 # Number of each molecule type
MOL:PRP:ATOM = 11 # Definition of the PRP molecule (propane)
# AtomId AtomName AtomCharge AtomMass
1 C1 -0.302 12.011
2 H11 0.068 1.0080
3 H12 0.068 1.0080
4 H13 0.068 1.0080
5 C2 0.270 12.011
6 H21 -0.037 1.0080
7 H22 -0.037 1.0080
8 C3 -0.302 12.011
9 H31 0.068 1.0080
10 H32 0.068 1.0080
11 H33 0.068 1.0080
MOL:PRP:MAPPING = 3 # Definition of the CG mapping of the PRP molecule
# BeadId BeadName BeadType : AtomIds
1 C1 CH3 : 1 2 3 4
2 C2 CH2 : 5 6 7
3 C3 CH3 : 8 9 10 11
MOL:PRP:BOND = 1 # Definition of the bonds in the CG PRP molecule
# BondTypeId : BeadId1 BeadId2 [, Beadid1 Beadid2 , ...]
1 : 1 2, 2 3
MOL:PRP:ANGLE = yes # if Yes, generates all types of angles in the molecule
MOL:PRP:DIHEDRAL = yes # if Yes, generates all types of dihedrals in the molecule
#############################
#############################
MOL:PRPO:ATOM = 12 # Definition of the PRP molecule (propane)
# AtomId AtomName AtomCharge AtomMass
1 C1 -0.287 12.011
2 H11 0.071 1.0080
3 H12 0.071 1.0080
4 H13 0.071 1.0080
5 C2 0.075 12.011
6 H21 0.001 1.0080
7 H22 0.001 1.0080
8 C3 0.239 12.011
9 H31 0.015 1.0080
10 H32 0.015 1.0080
11 O -0.688 15.9994
12 HO 0.416 1.0080
MOL:PRPO:MAPPING = 3 # Definition of the CG mapping of the PRP molecule
# BeadId BeadName BeadType : AtomIds
1 C1 CH3 : 1 2 3 4
2 C2 CH2 : 5 6 7
3 C3 CHO : 8 9 10 11 12
MOL:PRPO:BOND = 2 # Definition of the bonds in the CG PRP molecule
# BondTypeId : BeadId1 BeadId2 [, Beadid1 Beadid2 , ...]
1 : 1 2 # This bond is similar to the bond CH3-CH2 in molecule PRP (line28). So the id is set to 1
2 : 2 3
MOL:PRPO:ANGLE = yes # if Yes, generates all types of angles in the molecule
MOL:PRPO:DIHEDRAL = yes # if Yes, generates all types of dihedrals in the molecule