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