normal bulid a cg model for organics molecule

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5 months 2 weeks ago #9409 by LeMEI1
Hello,developer, recently, i built a cg model for organics molecule, and it could run the Energy minimisation and also converge. But when i run NVT, it shows the electrostatic and LJ equal to zero and i check i have loaded the martini_v3.0.0.itp. i have dealed with it a few days, not fixed it. Therefore, could you help me ?

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5 months 1 day ago #9431 by riccardo
Replied by riccardo on topic bulid a cg model for organics molecule
Hi, I lack some details on your system but I would first recommend to follow our tutorials and check if you are able to go through those without problems.

For example, the small molecule parametrization (since you mention "organic molecules", I'm assuming you are interested in modeling small molecules): cgmartini.nl/index.php/2021-martini-onli...a-new-small-molecule

But see this page for recent tutorials covering a wide range of Martini applications: cgmartini.nl/index.php/2021-martini-online-workshop/tutorials

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5 months 1 day ago #9432 by LeMEI1
Replied by LeMEI1 on topic bulid a cg model for organics molecule
Sorry to provide little information about my model. The ogranic molecule has 187 atoms and it owns a large plane. Before i use 'constraint' to fix them and the running has a lot of errors. However, i change it to bond connection and it looks good, But it just can run at a step of 1 fs and when i turn a large step, it also has mistakes, shown Warning: Triclinic box is too skewed.
Box (3x3):
Box[ 0]={-2.90043e+19, 0.00000e+00, 0.00000e+00}
Box[ 1]={-0.00000e+00, -2.90043e+19, -0.00000e+00}
Box[ 2]={-0.00000e+00, -0.00000e+00, -2.90043e+19}
Can not fix pbc.
so, do you have good approached to help me to fix it? Thank you so much~~~

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5 months 1 day ago #9433 by riccardo
Replied by riccardo on topic bulid a cg model for organics molecule
Hi, your model seems to be very numerically unstable. There is a quite detailed discussion of this problem in this paper: onlinelibrary.wiley.com/doi/pdf/10.1002/adts.202100391 (section "2.1.3. Advanced Model Design Strategies" and Figure 3). I would recommend to check that out.

You can find example of Martini 3 small-molecule models at: github.com/ricalessandri/Martini3-small-...all_molecules_v1.itp

However, there are no generic solutions to fixing numerical instabilities and your molecule seems quite large. I cannot provide much more help than this unless you share the structure and how your model looks like.

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5 months 15 hours ago #9434 by LeMEI1
Replied by LeMEI1 on topic bulid a cg model for organics molecule
I upload the structure of molecules both AA and CG. And the topology of molecules is created by myself manually. hopeful to receive your feedbck


github.com/LeLeMMM/ogranic-molecules . You can download them from the link. Thank you very much~~~

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4 months 3 weeks ago #9439 by riccardo
Replied by riccardo on topic bulid a cg model for organics molecule
I see. That's a tough - but very interesting! - one to model. I am happy to give you some feedback but that needs some discussion. If interested, write me at: alessandri [at] uchicago [dot] edu.

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