Peptide in water simulation vs circular dichroism (CD) results

User discussions
1

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.

Thank you,

Sanjiv Kumar

2

Dear sanjiv
The final conformation produced by gromacs is highly dependent to your initial structure. So, you have to be sure about the quality of your modeled structure that are used as the gromacs input. One strategy my be to modeled your structure using different software/servers, simulate deferent conformation of your structure, and then compare the stability of them.