I have a question on "tutorial.tcl" in espresso/samples folder.
In lines 168~186 (attached below), specifically in lines 168 and 185 (highlighted),
1)
what is "0" in line 168 (inter 0 fene 7.0 2.0)?
The user manual says it's "bondid" and I guess it's a bond between monomers.
But I don't see presetting for it anywhere in the tcl script. I mean it's all of sudden showed up.
If I have more than two types of bonds in a simulation,
can I just set different bondid for each and use like "inter $bond_1 fene 7.0 2.0", "inter $bond_2 harmonic 7.0 2.0"?
2)
what does "FENE 0" mean in line 185?
In user manual, I don't see FENE option for syntax "polymer".
If this means FENE interaction between monomers, would monomers interact via FENE potential TWICE ?
so, what are K and Rmax values for this FENE potential??
------------------------------------------------------------------------------------------------------------------
inter 0 fene 7.0 2.0
inter 0 0 lennard-jones 1.0 1.0 1.12246 0.25 0.0
inter 0 1 lennard-jones 1.0 1.0 1.12246 0.25 0.0
inter 1 1 lennard-jones 1.0 1.0 1.12246 0.25 0.0
#############################################################
# 5 Create Particles #
# Create the Polyelectrolyte and the counterions by using #
# the additional command 'polymer' and 'counterions'. #
# Use particle type 0 for the polyelectrolyte and 1 for #
# the counterions. #
# TIP: #
# You can control the result with the additional command #
# 'part', e.g: puts [part 10] prints information about #
# the particle with id 10 #
#############################################################
polymer 1 $l_poly 1.0 start 0 charge 1.0 types 0 0 FENE 0
counterions $n_ci start [setmd n_part] charge -1.0 type 1