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lammps/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt
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polymer.lt
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import "monomer.lt"
Polymer {
create_var {$mol} # optional:force all monomers to share the same molecule-ID
# (The "Data Atoms" in Monomer must use "$mol:..." notation.)
# Make a chain of monomers
monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0)
# Now, link the monomers together this way:
write("Data Bonds") {
$bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA
$bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA
$bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA
$bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA
$bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA
$bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA
$bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA
$bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA
$bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA
$bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA
$bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA
}
} # Polymer
# Angle, dihedral and improper interactions will be generated
# automatically according to the instructions in "monomer.lt"
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