Loop-Extrusion-Simulation/polymer_ff.xml at develop-common · lukaszmilewski/Loop-Extrusion-Simulation · GitHub

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<ForceField>

    <AtomTypes>
        <Type name="0" class="BEAD" element="B" mass="1"/>
    </AtomTypes>

    <Residues>

        <Residue name="BEC">
            <Atom name="B" type="0"/>
        </Residue>

        <Residue name="BEE">
            <Atom name="B" type="0"/>
            <ExternalBond from="0"/>
        </Residue>

        <Residue name="BEA">
            <Atom name="B" type="0"/>
            <ExternalBond from="0"/>
            <ExternalBond from="0"/>
        </Residue>

    </Residues>

    <CustomNonbondedForce energy="scale*((sigma1+sigma2)/r)^12" bondCutoff="0">
        <GlobalParameter name="scale" defaultValue="1"/>
        <PerParticleParameter name="sigma"/>
        <Atom type="0" sigma="0.05"/>
    </CustomNonbondedForce>

</ForceField>