Dear Christoph,
I have followed the option 1) Stop after 300 steps, change your
settings.xml (i.e. set do_potential to "0" for converged potentials) and go
on in the same directory structure.)
When I set do_potential to "0" for few of interactions, for example A-B,
the radial distributions are still moving. The attachment is the plot for
A-B RDFs from step_300 step and step_304.
Is this correct for "0" do_potential RDFs* still changing*? If it is
correct, what is the influence of "0 do_potential" in settings.xml?
Thank you.
Best regards,
Changwoon Jang
On Mon, Aug 8, 2016 at 1:55 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-08-08 10:26 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > Thank you for your comments. If I iterate only not converged
> potentials,
> > can I use the potentials converged over 300 steps?
> Yes!
>
> >
> >
> > Do I need to just modify the settings.xml file to iterate only not
> > converged RDFs? Do I just remove all converged RDFs,
> > <non-bonded>....</non-bonded>?
> Option 1a.) Stop after 300 steps, change your settings.xml (i.e. set
> do_potential to "0" for converged potentials) and go on in the same
> directory structure.
> Option 1b.) Copy <NAME>.pot.cur from step 300 to a new directory
> structure under the name <NAME>.pot.in and don't iterate them by
> setting do_potential to "0".
> Option 2.) Copy table_XXX.xvg to a new directory structure and remove
> the <non-bonded>....</non-bonded> for the or converged potentials.
>
> Christoph
> >
> >
> > Thank you very much.
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> >
> > On Mon, Aug 8, 2016 at 12:18 PM, Christoph Junghans <[email protected]>
> > wrote:
> >>
> >> 2016-08-08 9:26 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> > Dear Votca Users,
> >> >
> >> > I have run IBI for the system with 7 types of beads. Total 28
> >> > non-bonded
> >> > interactions.
> >> >
> >> > I have reached 500 steps. Each step runs about 8 ns (8000000
> >> > iterations).
> >> > Few of RDFs do not converge to the target RDFs. I keep running the IBI
> >> > but
> >> > the RDFs do not seem to be converged because the first peaks of new
> RDFs
> >> > do
> >> > not come down to the target peaks after 300 steps.
> >> >
> >> > Do I need to change some settings or do something else? Any comments
> are
> >> > appreciated.
> >> This is really system-depend! You could try to just iterate the
> >> interactions of the not converged RDFs starting from the potentials
> >> from step 300.
> >>
> >> Christoph
> >>
> >>
> >> >
> >> >
> >> > Thank you.
> >> >
> >> > Best regards,
> >> > Changwoon Jang,
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
> >> --
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> >
> >
> >
> >
> > --
> > Best regards,
> > Changwoon Jang,
> >
> > Postdoctoral Research Fellow
> > Department of Chemical & Biological Engineering, Drexel University
> > 3141 Chestnut Street, Philadelphia, PA 19104
> >
> > Voice: (662) 617-2267
> > E-mail: [email protected]
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
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--
Best regards,
Changwoon Jang,
Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104
Voice: (662) 617-2267
E-mail: [email protected]
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