Example: cgtraj.inp

This is an example of the input file, which reads a trajectory written in binary MDynaMix format stored in 10 files: dmpc16.001, dmpc16.002,...,dmpc16.010. The system presented in the trajectory consists of 16 DMPC lipid molecules dissolved in 1600 water molecules. The bead mapping scheme is shown on figure 2. The resulting CG DMPC have 10 beads. In the example below each water molecule will be represented by a single bead of ``CG water''. In order to completely remove the water and make implicit solvent model, the line beginning with H2O: should be commented out.

 &TRAJ
 NFORM='MDYN',
 FNAME='./MDynamix/dmpc16',
 PATHDB='./',
 NTYPES=2,
 NAMOL='dmpc_NM','H2O',
 NSPEC=16,1600,
 NFBEG=1,
 NFEND=10,
 ISTEP=1,
 IPRINT=6,
 &END


 BeadMapping
 CGTrajectoryOutputFile:cgtraj.001
  CGMolecularType:dmpc_NM.CG
    ParentType: dmpc_NM
    N:16:43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58
    P:11:59,60,61,62,63,64,65,66,67,68,69
    C1:9:1,2,3,4,5,73,74,75,76
    C2:12:6,7,8,9,10,11,12,13,14,15,16,17
    C3:12:18,19,20,21,22,23,24,25,26,27,28,29
    C4:13:30,31,32,33,34,35,36,37,38,39,40,41,42
    C5:8:70,71,72,77,78,79,80,81
    C6:12:82,83,84,85,86,87,88,89,90,91,92,93
    C7:12:94,95,96,97,98,99,100,101,102,103,104,105
    C8:13:106,107,108,109,110,111,112,113,114,115,116,117,118
  EndCGMolecularType 
  CGMolecularType:H2O.CG
    parenttype:H2O
    #comment the line below to exclude the water (make implicit solvent model)
    H2O:3:1, 2, 3
  endcgmoleculartype
EndBeadMapping

Figure 2: Simple mapping scheme of DMPC phospholipid, which consists of 118 atoms, into 10-beads CG model. The water is mapped into a single bead.