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

[Tristan Bereau]

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2) The user guide may be a little outdated in documenting some Espresso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