|
| From: | Nairhita Samanta |
| Subject: | Re: [ESPResSo-users] Pronlems with FENE bond |
| Date: | Tue, 1 Sep 2015 09:56:37 +0530 |
Hi there,
the response from Kai aimed at the part of your script where you insert
the "#Crowders". There you set up new particles starting from pid 0, which
is already occupied by a polymer particle, hence you delete a particle
from your polymer and hence the bonds break, in fact you relocate the
polymer beads beyond the FENE extensibility, because interactions and so
forth are not changed if the part command is called for an already
existing particle.
Kind regards,
Tobias
On Mon, August 31, 2015 16:52, Nairhita Samanta wrote:
> I removed the pid part from the polymer. But the same error message
> appears
> "background_errors { ERROR: bond broken between particles 3 and 2.
> Distance
> vector: 1.52436 10.2081 -8.71879 in function void
> add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 } { ERROR:
> bond broken between particles 7 and 6. Distance vector: -5.77841 -8.30212
> -11.8511 in function void add_bonded_force(Particle*)
> (forces_inline.hpp:903) on node 0 } { ERROR: bond broken between particles
> 4 and 3. Distance vector: -2.61192 0.75811 3.32631 in function void
> add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 } { ERROR:
> bond broken between particles 5 and 4. Distance vector: -10.3837 9.82012
> -0.23919 in function void add_bonded_force(Particle*)
> (forces_inline.hpp:903) on node 0 } { ERROR: bond broken between particles
> 2 and 1. Distance vector: 5.96483 1.0942 -6.3494 in function void
> add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 } { ERROR:
> bond broken between particles 6 and 5. Distance vector: -10.2424 -7.42658
> 9.36097 in function void add_bonded_force(Particle*)
> (forces_inline.hpp:903) on node 0 } { ERROR: bond broken between particles
> 8 and 7. Distance vector: -11.4322 6.64519 -7.67446 in function void
> add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 } { ERROR:
> bond broken between particles 1 and 0. Distance vector: -8.86446 -10.7269
> -8.23615 in function void add_bonded_force(Particle*)
> (forces_inline.hpp:903) on node 0 } { ERROR: bond broken between particles
> 9 and 8. Distance vector: 1.8256 0.81504 2.1973 in function void
> add_bonded_force(Particle*) (forces_inline.hpp:903) on node 0 }
> while executing
> "integrate $warm_steps"
> ("while" body line 2)
> invoked from within
> "while { $i < $warm_n_times && $act_min_dist < $min_dist } {
> integrate $warm_steps
>
> if { $vmd_online=="yes" } { imd positions }
> if { $vmd..."
> (file "pol3.tcl" line 221)"
>
> Attached is my tcl file.
>
> On Mon, Aug 31, 2015 at 7:03 PM, Kai Szuttor <address@hidden>
> wrote:
>
>> 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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