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Hi, All
I performed an asymmetric simulation (CG) of a lipid bilayer with a protein for 50 ns. However, a portion of the protein (yellow region) appears to have separated. Can anyone explain the possible reasons for this and suggest solutions to resolve the issue?
I had faced similar types of problems for md simulation of a protein in POPC lipid bilayer.
What do you mean with separated? Also 50ns are an extremely short simulation, especially in terms of CG models.
Hi
A yellow region of the protein appears to have separated (as seen in the screenshot) and is interacting with the surroundings. Can anyone explain why this is happening? Could it be due to improper embedding in the bilayer or protein instability?
Will increasing the simulation time help resolve this issue?
This should not be possible as if all beads belong to the same topology then they cannot separate. Can you plot the structures with their bonds as well so to see what is bound to what?
Also, if you are referring to the couple of yellow beads on the top centre of the box, are you sure these do not belong to the rest of the protein on the other side of the box, i.e., a pbc visualization issue?
Hi, sir
"Thank you for your suggestions.
After running the pbc unwrap command, the yellow beads did not separate.