normal Back mapping protocol

  • bikash
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6 years 10 months ago - 6 years 10 months ago #7261 by bikash
Back mapping protocol was created by bikash
Dear Members,

I am looking for a tutorial with an example of mapping of an all-atom structure to its corresponding CG model.

Could anyone please help me generating a CG model from my all-atom MD simulation?

Thanks in advance.

Sincerely,
Bikash
Last edit: 6 years 10 months ago by bikash.

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6 years 10 months ago #7265 by Pim
Replied by Pim on topic Back mapping protocol
Dear Bikash,

To avoid confusion: we call backmapping going from coarse-grain level back to all atom. What you seem to look for is actually (forward) mapping. You can find our tutorial here: cgmartini.nl/index.php/tutorials-general...rzining-new-molecule

If you want some additional tips you will have to show us your molecule.

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6 years 10 months ago - 6 years 10 months ago #7268 by bikash
Replied by bikash on topic Back mapping protocol
Dear Pim,

Thank you so much for your kind reply.

I have checked the "Parametrizing a new molecule based on known fragments"
earlier. But, I am unable to start and need some guidance to learn it. As requested, I am uploading the molecule of my interest. Please kindly check the link ( Molecule ) to view the structure.



I am looking forward to your kind response.


Thanking you in advance.

Sincerely,
Bikash
Last edit: 6 years 10 months ago by bikash. Reason: Mistyped

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6 years 10 months ago #7269 by Pim
Replied by Pim on topic Back mapping protocol
That's fairly tricky. What exactly do you not understand on how to proceed?

I would map the phenyl + backbone carbon as 3 S-beads, the amide and backbone carbon and the remaining ethanol as 2 beads and the aldehyde + 2 backbone beads as one bead.

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