rdf does not fall to one during ibi in polymer system

[Saeed Norouzi]

Dear developers,

I am trying to run IBI using csg_inverse --options settings.xml, and all necessary information is attached below. my RDF does not go to 1 during ibi iteration. Can you please help me with what is wrong?

[Christoph Junghans]

On Fri, Nov 18, 2022 at 7:19 AM Saeed Norouzi <norou...@gmail.com> wrote:
>
> Dear developers,
>
> I am trying to run IBI using csg_inverse --options settings.xml, and all necessary information is attached below. my RDF does not go to 1 during ibi iteration. Can you please help me with what is wrong?

Looks to me like you need to increase the box size and just sample the
RDF to a higher radius. (in the target setup)
Also a step of 0.005 seems a bit too fine, try 0.01 as a start, only
make it finer if you can resolve a peak.

Christoph

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--
Christoph Junghans
Web: http://www.compphys.de

[Saeed Norouzi]

Dear Christoph,

Thank you for your reply, I tried those but did not work, and still, the RDF increases during ibi iteration.

Best regards

Saeed

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[Christoph Junghans]

On Fri, Nov 18, 2022 at 11:55 AM Saeed Norouzi <norou...@gmail.com> wrote:
>
> Dear Christoph,
>
> Thank you for your reply, I tried those but did not work, and still, the RDF increases during ibi iteration.

Maybe I am misunderstanding, but your target RDF doesn't go to 1.0,
which has nothing to do with IBI or VOTCA.

Christoph

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[Saeed Norouzi]

Dear Christoph,

I appreciate your help. 

My AA RDF was not correct now it works and the CG RDF matches with AA. I have another question, the RDF for non-boned is matched and I did a pressure correction also to have the correct pressure and density. But the distribution bond, angle, and dihedral do not match with the target all-atom model. should I do the ibi for bonded interactions also? if so, should I first do the iteration for bonded interaction and then for nonbonded or vice versa? or at the same time? 

Best regards

Saeed

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[Marvin Bernhardt]

Hello Saeed

Yes, you can also optimize bond and angle potentials such that the distributions match the atomistic simulation. In my experience, optimizing everything at the same time is not ideal, as it can prevent convergence. Optimizing bonded and non-bonded interactions alternately will more likely work. See this tutorial and the `do_potential` option.

Cheers,
Marvin

[Saeed Norouzi]

Hi Marvin,

Thank you for your suggestion.

Best regards

Saeed

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