GROMACS version: 2022
GROMACS modification: No
Circular dichroism (CD) data for the peptides in water shows random coils but alpha helical in organic solvents.
I am using a folded peptide (alpha helical by modelling) to perform peptide in water simulation, during the whole run 1000 ns, the peptide retains alpha helical structure.
Is there an explanation for the discrepancy between the two results (CD vs MD simulation). How do I show using MD that the peptide in water is indeed random coil, if that is correct?
It would be helpful if I can be guided to some literature.