The bead mapping scheme is shown on figure 2.
Note that the resulting CG DMPC molecule has 10 beads, while each water molecule will be represented by a single bead. In order to completely remove the water (implicit solvent) you shall comment out the water-related bead mapping section. The output trajectory format is defined by the extension of the CGTrajectoryOutputFile
file.
[fontsize=\small] &TRAJ NFORM='XTC', FNAME='dmpc_all_atom_trajectory.xtc', NTYPES=2, NAMOL='dmpc_NM','H2O', NSPEC=16,1600, &END BeadMapping CGTrajectoryOutputFile:dmpc_cgtraj.xtc CGMolecularType:dmpc_NM.CG ParentType: dmpc_NM N:16:43-58 P:11:59-69 C1:9:1-5,73-76 C2:12:6-17 C3:12:18-29 C4:13:30-42 C5:8:70-81 C6:12:82-93 C7:12:94-105 C8:13:106-118 EndCGMolecularType CGMolecularType:H2O.CG ParentType:H2O #comment the line below to exclude the water completely H2O:3:1, 2, 3 EndCGMolecularType EndBeadMapping