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Re: [ESPResSo] Restarting a Simulation


From: Salvador Herrera Velarde
Subject: Re: [ESPResSo] Restarting a Simulation
Date: Mon, 12 Apr 2010 17:35:18 -0500

Hi Axel,
Thanks a lot for your answer.

I just have one more question.

If a want to start a new simulation with box length say {30 30 30} and I need the coordinates from a previous simulations via: 
$last_configuration.gz" {time box_l npt_p_diff } {id pos type v f molecule}.
The coordinates in this file (last_configuration.gz) are outside of the box size 30 30 30 because of they are unfolded.  So, how ESPResSo treats these coordinates in my new box simulation [30 30 30]? 

Thanks a lot for your time,

Salvador

----- Original Message -----
From: Axel Arnold <address@hidden>
Date: Friday, April 9, 2010 3:15 am
Subject: Re: [ESPResSo] Restarting a Simulation
To: address@hidden

> On Thursday 08 April 2010 22:05:43 Salvador Herrera Velarde wrote:
> > Hi All,
> >
> > First of all, thanks to ALL users and developers for your time
> and help
> > with all my questions.
> >
> > I using mbtools to run  a simulation which contains a
> large chain of
> > monomers among other molecules.
> >
> > I want to restart the simulation with different conditions; to
> save the
> > actual configuration I was using the command: polyBlockWrite
> > "$outputdir/$ident.[format %04d $j].gz" {time box_l npt_p_diff
> } {id pos
> > type v f molecule}
> >
> > Then, I used the generated file to restart the simulation.
> However,  when I
> > visualized the snapshots in VMD, there are many bonds spanning
> along the
> > box simulation. I think this is an effect of the periodic boundary
> > conditions. To fix the problem I tried to fold the positions:
> > polyBlockWrite "$outputdir/$ident.[format %04d $j].gz" {time box_l
> > npt_p_diff } {id folded_position type v f molecule}
> >
> > But still the same problem.
> >
> > Does anybody has an idea of how to fix the problem?
>
> First of all, for almost all purposes it is better to save the
> unfolded
> position in your blockfiles, since for example mean square
> displacements are
> otherwise incorrectly sampled after restarting. So, the first
> version is the
> way you want to save your data.
>
> Regarding the spanning bonds - that has nothing to do how
> Espresso internally
> stores the coordinates, therefore you get exactly the same
> output whether you
> use folded or positions in your blockfiles. This is indeed just
> a problem of
> visualization. Due to the periodic boundary conditions, you
> always will have
> bonds spanning the whole box when drawn nonperiodic. So, what
> you would need
> is a way to dynamically hide bonds which are longer than a
> certain length, but
> that VMD can't do as far as I know. Alternatively, if there is a
> concept of
> molecules in your setup, you can try to fold each of the
> molecules
> consistently according to its center of mass; look at Olaf's
> pbctools how to
> do that (http://www.espresso-pp.de/projects/pbctools).
>
> Cheers,
> Axel
>
>
>
> --
> Dr. Axel Arnold Tel: +49 711 685 67609
> ICP, Universit├Ąt Stuttgart      Email:
> address@hidden
> Pfaffenwaldring 27
> 70569 Stuttgart, Germany
>
>
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