Re: [ESPResSo-users] question on "tutorial.tcl"

[Tristan Bereau]

No, it doesn't interact twice: the first line creates a FENE interaction
with certain parameters. At that point it is _not_ associated to any
particles. It's the second line that associates interaction FENE "0"
with the relevant particles. You might want to have a look at the
example "harmonic-oscillator" to see how the bonded interaction (a
harmonic spring, this time) is associated to the particles using the
command 'part'. It's probably a more transparent call, compared to the
"polymer" command.

Best,
Tristan

On 01/07/2011 03:32 PM, Edward Kim wrote:
> So, that means the simulated polymer does _not_ interact _twice_ via
> FENE.
> In other words, the two lines are just necessary to make polymer
> (group of particles) interact via FENE potential, right?
>
> Thank you so much.
> Have a good weekend!
>
>
> On Fri, Jan 7, 2011 at 3:20 PM, Tristan Bereau <address@hidden
> <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     2) The user guide may be a little outdated in documenting some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
>
>