.mcm file example: DMPC.CG.mcm

The mcm-file listed below defines 10-beads model of DMPC-lipid, as shown on figure .

Figure: Example: 10-beads CG model of DMPC-lipid. Beads and bonds of same color have same type; solid lines denote covalent bonds; dashed arrows denote angle bending bonds.

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#Number of atoms
10
# Name   X     Y       Z      Mass   Q  NumofType NameofType    
N    -6.1804 -17.2679 17.2781 73.139 0.76 1 N
P    -9.6995 -17.2121 14.915 123.0256 -0.89 2 P
C2   -18.1023 -13.2828 10.2371 56.108 -0.0 3 CH
C3   -21.9375 -11.5562 7.3382 56.108 -0.0 3 CH
C4   -24.5552 -9.7683 3.2938 57.116 -0.0 3 CH
C6   -15.3122 -17.1232 8.1441 56.108 -0.0 3 CH
C7   -18.7644 -15.0198 5.1392 56.108 -0.0 3 CH
C8   -21.6201 -13.2988 1.0155 57.116 -0.0 3 CH
C1   -14.7182 -15.6667 12.7078 72.0638 -0.09 4 CO
C5   -13.3132 -18.7418 11.2877 71.0558 0.22 4 CO
#
# Here we define covalent like bonds
# Total number of covalent bond types: 5
5
# Covalent bond N-P
# One atom pair belongs to covalent bond type 1
1
# Define pair of atoms by their numbers in the list above: 1 (N) 2 (P),
# the third number should always be 1 for covalent bond.
1  2  
# Covalent bond P-CO
# Two atom pairs belong to covalent bond type 2
2
# Define 2 pairs of atoms by their numbers in the list above: 2 (P) and 9,10 (C1,C5)
2  9  
2  10  
# Covalent bond CH-CH
# Four atom pairs belong to covalent bond type 3
4
# Define 4 pairs of atoms by their numbers in the list above: 3-4, 4-5, 6-7, 7-8
3  4  
4  5  
6  7  
7  8  
# Covalent bond type 4
2
9  3  
10  6  
# Covalent bond type 5
1
9  10  
#
# Here we define angle bending bonds
# Total number of angle bending bonds:5
5
# Two atom triplets belong to angle bond type 1: 
2
1  2  9  
1  2  10  
# Two atom triplets belong to angle bond type 2: 
2
2  9   3  
2  10  6  
# angle bond type 3: 
2
9  3  4  
10  6  7  
# angle bond type 4: 
2
3  4  5 
6  7  8 
# angle bond type 3: 
2
3  9  10  
6  10  9