> <mailto:
address@hidden>> wrote:
>
> Hi Edward,
>
> 1) The "0" of the "inter 0 fene 7.0 2.0" command is indeed the name or
> ID of that bond. It's just an identifier. It's used to define the
> bonded
> interaction between monomers, as stated in the second command you
> overlined: "polymer 1 $l_poly...". The argument "FENE 0" means it's
> using that FENE bond as a bonded interaction. In general, you'd
> use the
> 'part' command to register bonded interactions between particles. See
> the user guide.
>
> 2) The user guide may be a little outdated in documenting some
> Espresso
> commands. In case of doubt, it's always best to dig into the code. To
> answer the last part of your question, the K and Rmax of the FENE
> potential are described in the initialization of ID "0" of the
> FENE bond
> (the first command you overlined). The fact that "polymer..." calls
> "FENE 0" means it's calling ID 0 of a FENE interaction, thus
> calling its
> parameters.
>
> Best,
> Tristan
>
> On 01/07/2011 03:07 PM, Edward Kim wrote:
> > Hello,
> > 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
>
>