Example: cgtraj.inp

This is an example of the input file, which reads a trajectory in binary XTC format. The system presented in the trajectory, consists of 16 DMPC lipid molecules solved in 1600 water molecules.

**Figure 2:** Mapping scheme for DMPC phospholipid, which consists of 118 atoms, into 10-beads CG model. The water is mapped into a single bead.
$\includegraphics[scale=0.20]{.././files/DMPC_CG_example-125ps.pdf}$

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