[ESPResSo-users] multiple potentials on a polymer

[Edward Kim]

Hello,

I have a newbie question.
I'd like to apply more than two potentials on a polymer chain.

It seems that syntax "polymer" doesn't have an option for multiple potentials.

So, can I just make a script like below ?

Which is correct, (1) or (2) ??

By the way,

Could I use an user-defined potential (which is not defined in Espresso)?

If so, would anyone let me know how to?

Thank you.

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To simulate LJ + FENE + Harmonic potentials on a polymer chain,

(1)

set monomer_id    0

set monomer_charged_id    1

set bondid_fene  5

set bondid_harmonic  6

inter $monomer_charged_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $monomer_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $monomer_id $monomer_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $bondid_fene fene $fene_k $fene_r

inter $bondid_harmonic harmonic $k_spring $r_eq

polymer $n_polymers $n_monomers $bond_length mode SAW $shield $max_try charge $charge_monomer distance $dist_charge types $monomer_id $monomer_charged_id bond $bondid_fene

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(2)

set monomer_id    0

set monomer_charged_id    1

set bondid_fene  5

set bondid_harmonic  6

inter $monomer_charged_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $monomer_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $monomer_id $monomer_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off

inter $bondid_fene fene $fene_k $fene_r

inter $bondid_harmonic harmonic $k_spring $r_eq

for { set i 0 } { $i < $n_monomers } { incr i } { 

    if {[expr $i%$dist_charge]==0} {

          set ix [expr $box_l*[t_random]]

          set iy [expr $box_l*[t_random]]

  set iz [expr $box_l*[t_random]]

          part $i pos $ix $iy $iz bond $bondid_fene [expr $i+1] q $charge_monomer type $monomer_charged_id

          part $i pos $ix $iy $iz bond $bondid_harmonic [expr $i+1] q $charge_monomer type $monomer_charged_id

    } else {

set ix [expr $box_l*[t_random]]

set iy [expr $box_l*[t_random]]

set iz [expr $box_l*[t_random]]

part $i pos $ix $iy $iz bond $bondid_fene [expr $i+1] type $monomer_id

        part $i pos $ix $iy $iz bond $bondid_harmonic [expr $i+1] type $monomer_id

    }

}

part $i

polymer $n_polymers $n_monomers $bond_length mode SAW $shield $max_try charge $charge_monomer distance $dist_charge types $monomer_id $monomer_charged_id bond $bondid_fene