Mismatch between target bonded interaction and IBI result

[Lucia Hsu]

Dear all,

I hope this message finds you well. I am currently working on utilizing VOTCA for conducting an  IBI analysis on a system composed of 500 molecules. Each molecule is represented by a sequence of three beads arranged as A-B-A. To perform this analysis, I have been following the cgs-tutorials/hexane/ibi_all guide, aiming to obtain the bonded interaction (A-B), the angle (A-B-A), and the nonbonded interactions (A_A, A_B, B_B) within my system.

However, I have encountered some discrepancies in the output results, particularly regarding the bonded interactions. Upon inspecting the plotted angle/bond/RDF for the first step 001, I have observed a significant deviation from the target values represented by the black line. I am reaching out to seek the expertise of anyone who can provide valuable advice on how to address and correct this issue.

I would greatly appreciate any guidance or suggestions you can provide to help me rectify this situation. Thank you very much for your attention and support.

Best regards,
Lucia

[Christoph Junghans]

On Mon, Mar 18, 2024 at 5:18 AM Lucia Hsu <wqxu...@gmail.com> wrote:

Dear all,

I hope this message finds you well. I am currently working on utilizing VOTCA for conducting an  IBI analysis on a system composed of 500 molecules. Each molecule is represented by a sequence of three beads arranged as A-B-A. To perform this analysis, I have been following the cgs-tutorials/hexane/ibi_all guide, aiming to obtain the bonded interaction (A-B), the angle (A-B-A), and the nonbonded interactions (A_A, A_B, B_B) within my system.

However, I have encountered some discrepancies in the output results, particularly regarding the bonded interactions. Upon inspecting the plotted angle/bond/RDF for the first step 001, I have observed a significant deviation from the target values represented by the black line. I am reaching out to seek the expertise of anyone who can provide valuable advice on how to address and correct this issue.

I would greatly appreciate any guidance or suggestions you can provide to help me rectify this situation. Thank you very much for your attention and support.

First of all, your targets look very rough, I guess you need to run your all-atom simulation a bit longer (or make the bin size bigger).

Second, I would start with the ibi on the non-bonded only and use the BI potentials for the bonds first and then iterate on them later.

That might help with the bond distribution.

Christoph

Best regards,
Lucia

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