- Posts: 6
backmapped structure not the same as the Initial starting structures
- aishwarya
-
Topic Author
- Offline
- Fresh Boarder
Less
More
4 years 10 months ago - 4 years 10 months ago #8155
by aishwarya
backmapped structure not the same as the Initial starting structures was created by aishwarya
Hi martini users.
I want to simulate a system composed of 10 peptides with the same initial structures. I performed the martini mapping and then, without performing any dynamics, I backmapped the structures. The backmapped structures (Using initram-v5.sh) are not exactly the same as the initial structure and they are different among them. This results is a bit wierd to me. Is there a way to obtain always the same structure from the backmapping? What is missing?
Thanks in advance
Aishwarya
I want to simulate a system composed of 10 peptides with the same initial structures. I performed the martini mapping and then, without performing any dynamics, I backmapped the structures. The backmapped structures (Using initram-v5.sh) are not exactly the same as the initial structure and they are different among them. This results is a bit wierd to me. Is there a way to obtain always the same structure from the backmapping? What is missing?
Thanks in advance
Aishwarya
Last edit: 4 years 10 months ago by aishwarya.
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
4 years 10 months ago #8156
by riccardo
Replied by riccardo on topic backmapped structure not the same as the Initial starting structures
Hi,
The backmapping consists of two steps: a projection based on the mapping files and a relaxation (a few energy minimizations and short MD simulations). Te second step (relaxation) involves some randomness, so I wouldn't be surprise if the backmapped structures are not exactly the same.
But I'm not sure I understand which system you want to simulate: if it's 10 peptides having the same conformation randomly placed in a box, I'd backmap one of them and then place 10 of these conformations in a box (with gmx insert-molecules, etc.). But probably you want to do something different?
The backmapping consists of two steps: a projection based on the mapping files and a relaxation (a few energy minimizations and short MD simulations). Te second step (relaxation) involves some randomness, so I wouldn't be surprise if the backmapped structures are not exactly the same.
But I'm not sure I understand which system you want to simulate: if it's 10 peptides having the same conformation randomly placed in a box, I'd backmap one of them and then place 10 of these conformations in a box (with gmx insert-molecules, etc.). But probably you want to do something different?
Please Log in or Create an account to join the conversation.
- aishwarya
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 6
4 years 10 months ago #8157
by aishwarya
Replied by aishwarya on topic backmapped structure not the same as the Initial starting structures
Thank you for your reply. We wanted to monitor changes on the peptide structures during the MD trajectory. To address this problem, we started employing the procedure mentioned before in order understand if the uncertainty we have with the backmapping procedure is less than the one we have for the structures that are in the CG representation are considerably different.
Please Log in or Create an account to join the conversation.
- tsjerk
-
- Offline
- Expert Boarder
Less
More
- Posts: 103
4 years 10 months ago #8158
by tsjerk
Replied by tsjerk on topic backmapped structure not the same as the Initial starting structures
Please try the Github version:
www.github.com/tsjerk/Backward
The structure may deviate a bit, because information is lost upon coarse-graining. However, the difference should not be very large. If the problem persists with the newest (github) version, please send me the structure before and after.
The structure may deviate a bit, because information is lost upon coarse-graining. However, the difference should not be very large. If the problem persists with the newest (github) version, please send me the structure before and after.
Please Log in or Create an account to join the conversation.
- aishwarya
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 6
4 years 10 months ago #8159
by aishwarya
Replied by aishwarya on topic backmapped structure not the same as the Initial starting structures
Thank you for your suggestion and reply.
Please Log in or Create an account to join the conversation.
Time to create page: 0.153 seconds