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Re: [ESPResSo-users] Pronlems with FENE bond


From: Nairhita Samanta
Subject: Re: [ESPResSo-users] Pronlems with FENE bond
Date: Mon, 31 Aug 2015 18:51:55 +0530

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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