Re: [ESPResSo-users] Pronlems with FENE bond

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
> >> > >
> >> > >
> >>
> >
> >

From:	Nairhita Samanta
Subject:	Re: [ESPResSo-users] Pronlems with FENE bond
Date:	Mon, 31 Aug 2015 18:43:00 +0530