- Posts: 105
Back mapping protocol
- bikash
- Topic Author
- Visitor
6 years 11 months ago - 6 years 11 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
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 11 months ago by bikash.
Please Log in or Create an account to join the conversation.
- Pim
- Offline
- Expert Boarder
Less
More
6 years 11 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.
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.
Please Log in or Create an account to join the conversation.
- bikash
- Topic Author
- Visitor
6 years 11 months ago - 6 years 11 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
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 11 months ago by bikash. Reason: Mistyped
Please Log in or Create an account to join the conversation.
- Pim
- Offline
- Expert Boarder
Less
More
- Posts: 105
6 years 11 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.
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.
Please Log in or Create an account to join the conversation.
Time to create page: 0.096 seconds