Re: [ESPResSo-users] Pronlems with FENE bond

[Kai Szuttor]

To first use the harmonic bond is a little "overkill". As far as i can
see you first use the polymercommand which starts creating particles
with pid 0. After that you're overwriting the positions of these particles
manually.

Cheers,

Kai

PS: theres also a sample in the source in the directory
samples/pe_solution.tcl
On Mon, Aug 31, 2015 at 06:51:55PM +0530, Nairhita Samanta wrote:
> Hi Tristan!
> Is there any way I can generate bonds within the FENE length in the first
> place? i have just started using espresso and I doubt whether I can execute
> what you suggested.
> 
> On Mon, Aug 31, 2015 at 6:46 PM, Tristan Bereau <address@hidden>
> wrote:
> 
> > Hi Nairhita,
> >
> > Then why not run it first with harmonic bonds, equilibrate it, save
> > the configuration, and then use that as initial configuration for the
> > FENE simulation. What you describe sounds like the polymer you
> > initially generate creates bonds beyond the FENE length.
> >
> > Cheers,
> > Tristan
> >
> > On Mon, Aug 31, 2015 at 3:13 PM, Nairhita Samanta <address@hidden>
> > wrote:
> > > Please find the attached. And it is working when I use harmonic bonds in
> > the
> > > polymer.
> > >
> > > On Mon, Aug 31, 2015 at 6:37 PM, Kai Szuttor <address@hidden>
> > > wrote:
> > >>
> > >> Hi,
> > >>
> > >> maybe we could better help, if you attach the whole script.
> > >> The snippet in your email should not be the problem (although your doin
> > >> some weird stuff with that for-loop).
> > >>
> > >> Cheers,
> > >>
> > >> Kai
> > >> On Mon, Aug 31, 2015 at 06:31:22PM +0530, Nairhita Samanta wrote:
> > >> > Hi everyone!
> > >> > I am still getting the same error (background_errors { ERROR: bond
> > >> > broken
> > >> > between particles 3 and 2...) when I use the following command
> > >> >
> > >> >
> > >> >
> > >> > set pid 0
> > >> > append vtf_bonds "polymer"
> > >> > polymer 1 $nummon $b_l start $pid mode RW bond 2
> > >> >  set start_pid $pid
> > >> > for {set i 0} { $i < $nummon } {incr i} {
> > >> >    incr pid}
> > >> > set end_pid [expr $pid-1]
> > >> >     append vtf_bonds "bond " $start_pid "::" $end_pid "\n"
> > >> >
> > >> > Regards,
> > >> > Nairhita
> > >> >
> > >> > On Mon, Aug 31, 2015 at 5:45 PM, Nairhita Samanta <
> > address@hidden>
> > >> > wrote:
> > >> >
> > >> > > Okay I got it. Thank you for your reply Kai.
> > >> > >
> > >> > > On Mon, Aug 31, 2015 at 5:43 PM, Kai Szuttor
> > >> > > <address@hidden>
> > >> > > wrote:
> > >> > >
> > >> > >> Please have a look at the UG at page 35 (in the current dev UG).
> > >> > >> You dont need to explicitly set the position of the monomers if
> > youre
> > >> > >> using the "polymer" command.
> > >> > >>
> > >> > >> Cheers,
> > >> > >>
> > >> > >> Kai
> > >> > >> On Mon, Aug 31, 2015 at 05:40:05PM +0530, Nairhita Samanta wrote:
> > >> > >> > Thank you Florian for your reply. Yes I would definitely answer
> > in
> > >> > >> > the
> > >> > >> > mailing list from now on.
> > >> > >> >
> > >> > >> > So is it like if I mention a bond-length for the polymer, the
> > >> > >> > 'polymer'
> > >> > >> > command will automatically put the monomers accordingly. In that
> > >> > >> > case I
> > >> > >> > don't need to "set the position" for the monomers. Or do I need
> > to?
> > >> > >> >
> > >> > >> > On Mon, Aug 31, 2015 at 4:33 PM, Florian Weik <
> > >> > >> address@hidden>
> > >> > >> > wrote:
> > >> > >> >
> > >> > >> > > On Mon, Aug 31, 2015 at 12:54 PM, Nairhita Samanta <
> > >> > >> address@hidden>
> > >> > >> > > wrote:
> > >> > >> > >
> > >> > >> > >> I assumed this way all the particles will be in a distance
> > >> > >> approximately
> > >> > >> > >> $b_l from each other. So how do I position the monomers?
> > >> > >> > >> According
> > >> > >> to box
> > >> > >> > >> length?
> > >> > >> > >>
> > >> > >> > >> "set posx [expr $b_l*rand()]
> > >> > >> > >> set posy [expr $b_l*rand()]
> > >> > >> > >> set posz [expr $b_l*rand()]" is it defining all the monomers
> > or
> > >> > >> > >> just
> > >> > >> the
> > >> > >> > >> starting one? I am confuse with this command.
> > >> > >> > >>
> > >> > >> > >> On Mon, Aug 31, 2015 at 4:17 PM, Florian Weik <
> > >> > >> address@hidden
> > >> > >> > >> > wrote:
> > >> > >> > >>
> > >> > >> > >>> Hi,
> > >> > >> > >>> you are putting all particles in a sphere of radius of $b_l
> > >> > >> > >>> about
> > >> > >> the
> > >> > >> > >>> origin. Is this really what you want?
> > >> > >> > >>> If you have other interactions, for example a Lennard-Jones,
> > >> > >> > >>> this
> > >> > >> will
> > >> > >> > >>> probably explode, if you have a
> > >> > >> > >>> typical time step.
> > >> > >> > >>>
> > >> > >> > >>> Cheers,
> > >> > >> > >>> Florian
> > >> > >> > >>>
> > >> > >> > >>
> > >> > >> > >>
> > >> > >> > > The polymer command actually creates the particles, the
> > positions
> > >> > >> > > are
> > >> > >> > > chosen by a random walk with step length $b_l (because you said
> > >> > >> > > so).
> > >> > >> > > If you have no other interactions what you did should still
> > work,
> > >> > >> maybe
> > >> > >> > > you need to reduce you time step.
> > >> > >> > >
> > >> > >> > > Please answer to the mailing list and not to me personally
> > >> > >> > > ('Answer to
> > >> > >> > > all'), so everybody can read profit from the conversation.
> > >> > >> > >
> > >> > >> > > Cheers,
> > >> > >> > > Florian
> > >> > >> > >
> > >> > >> > > --
> > >> > >> > > Florian Weik, Dipl.-Phys.,
> > >> > >> > > Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
> > >> > >> > > Phone: +49-711-685-67703
> > >> > >> > > Public Key 0x0562F11D Fingerprint 3294 6360 EC93 37A3 BD40
> > F597
> > >> > >> > > 0BAD
> > >> > >> 3AF8
> > >> > >> > > 0562 F11D
> > >> > >> > >
> > >> > >> > >
> > >> > >>
> > >> > >
> > >> > >
> > >
> > >
> >

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