- Posts: 30
The insertion difference between all-atom and coarse-grained
- roshanak
-
Topic Author
- Offline
- Junior Boarder
Less
More
6 years 3 months ago #7473
by roshanak
The insertion difference between all-atom and coarse-grained was created by roshanak
Hi everybody
I simulated one peptide on the POPE:POPG membrane with all-atom and coarse-grained scale. The coarse-grained system included 252:48 POPE:POPG and the all-atom system had 96:32. I wanted to investigate the peptide insertion into the membrane. In the CG system, I saw after (almost) 20 nanoseconds the peptide inserted into the membrane and in the all-atom system, it happened thereabout. In the both of systems, the peptide remained in the nearly constant distance until the end of 1 microseconds. In CG, insertion occurred more than all-atom systems (about 0.5 nanometers!!!). I used SPC water and gromos53a96 forcefield in all-atom and polarizable forcefield (martinize 22p) and polarizable water in CG.
Now, my question is: why does the peptide in the CG insert more than all-atom?
Is it due to electrostatic in polarizable forcefield or another thing?
I simulated one peptide on the POPE:POPG membrane with all-atom and coarse-grained scale. The coarse-grained system included 252:48 POPE:POPG and the all-atom system had 96:32. I wanted to investigate the peptide insertion into the membrane. In the CG system, I saw after (almost) 20 nanoseconds the peptide inserted into the membrane and in the all-atom system, it happened thereabout. In the both of systems, the peptide remained in the nearly constant distance until the end of 1 microseconds. In CG, insertion occurred more than all-atom systems (about 0.5 nanometers!!!). I used SPC water and gromos53a96 forcefield in all-atom and polarizable forcefield (martinize 22p) and polarizable water in CG.
Now, my question is: why does the peptide in the CG insert more than all-atom?
Is it due to electrostatic in polarizable forcefield or another thing?
Please Log in or Create an account to join the conversation.
- Pim
-
- Offline
- Expert Boarder
Less
More
- Posts: 105
6 years 3 months ago #7475
by Pim
Replied by Pim on topic The insertion difference between all-atom and coarse-grained
That's difficult to say, but I'd say 0.5 nm is not such an enormous difference considering the size of a Martini bead (0.47 nm), it means the peptide is one bead shifted into the bilayer. Perhaps your different membrane composition has something to do with it (5.25:1 vs 3:1, so less negative charge in the CG system), but that doesn't have to be it. If there is a charged residue at the interface, that may point you in the direction of the answer.
Please Log in or Create an account to join the conversation.
- roshanak
-
Topic Author
- Offline
- Junior Boarder
Less
More
- Posts: 30
6 years 3 months ago #7476
by roshanak
Replied by roshanak on topic The insertion difference between all-atom and coarse-grained
Thanks for replying
Excuse me, I made a mistake. That's not 252:48. That's 252:84. In CG and AA rate of lipids is 3:1.
What do you mean by charged residue? Is it about amino acids? The peptide has an amidated C-terminal and a positive amino acid in its N-terminal.
Excuse me, I made a mistake. That's not 252:48. That's 252:84. In CG and AA rate of lipids is 3:1.
What do you mean by charged residue? Is it about amino acids? The peptide has an amidated C-terminal and a positive amino acid in its N-terminal.
Please Log in or Create an account to join the conversation.
Time to create page: 0.098 seconds