Skip to content

Polymerization of monomer with two heads and tails #35

Description

@supriyonaskar

Dear Developers,
I would like to build a polymer (Like PIM-1) with two heads and two tails. I can find examples with single head and tail and procedures to assign them. However, I am finding it difficult to define two heads in the code. Could you please provide some examples?

If you can please edit the following code to assign two heads that would be great.

def monomer():

    s = system.read_mol('My.mol'))
    m = s.molecules[1]
    f = forcefield.Gaff2()
    
    for b in s.bonds:
        if b.a.bonds.count == 3 and b.b.bonds.count == 3:
            b.order = 4
    
    s.apply_forcefield(f)
    
    c1 = s.particles[1] #head 1
    c2 = s.particles[2]  #head 2

    c5 = s.particles[5] #tail 1
    c5 = s.particles[6]  #tail 2

    
    for b in c1.bonds:
        if b.a.elem == 'H' or b.b.elem == 'H':
            pb = b.a if b.b is c1 else b.b
            s.particles.remove(pb.tag, update=False)
            break
        
    for b in c5.bonds:
        if b.a.elem == 'H' or b.b.elem == 'H':
            pb = b.a if b.b is c1 else b.b
            s.particles.remove(pb.tag, update=False)
            break
            
    s.remove_spare_bonding()

    c1.linker = 'head'
    #c2.linker= 'head'
    c5.linker = 'tail'
    #c6.linker= 'tail'
    
    lmps.quick_min(s, min_style='fire')
    
    s.add_particle_bonding()
    
    return s

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions