Example: rdf.inp

This is an example of rdf.inp file which defines reference distribution function calculation for a CG lipid model with interactions shown on figure 3.

[fontsize=\footnotesize]
&Parameters
 TrajFile = cgtraj.dmpc16-400ns.xmol
 NMType = 1
 NameMType = dmpc_NM.CG.mmol
 NMolMType = 16
 OutputFile = dmpc16-100aa.rdf
 RMaxNB = 20.
 RMaxB =10.0
 ResolNB =0.1
 ResolB=0.02
 ResolA=1.0
&ENDParameters

&CGTypes
N:N
P:P
CH:C2 C3 C4 C6 C7 C8
CO:C1 C5
&EndCGTypes

&RDFsNB
Add: all
# Add: N--P
# Add: N--P: N P
# Add: N--CO: N C1, N C5 
&EndRDFsNB

&RDFsB
add: dmpc_NM.CG: 1: N P
add: dmpc_NM.CG: 2: P C1, P C5
add: dmpc_NM.CG: 3: C2 C3, C3 C4, C6 C7, C7 C8
add: dmpc_NM.CG: 4: C1 C2, C5 C6
add: dmpc_NM.CG: 5: C1 C5
&EndRDFsB

&RDFsA
Add: all
#add: dmpc_NM.CG: All #Other way - generate all A-bonds for the molecule
#add: dmpc_NM.CG: 6: N P C1 #Example - create N-P-CO A-bond
&EndRDFsA

&SameAsBond
# Empty
&EndSameAsBond

Figure 3: Example: 10-beads CG model of a DMPC lipid. Beads and bonds of the same color have same type; solid lines denote covalent bonds; dashed arrows denote angle bending bonds.