[gmx-users] Calculating Eccentricity

[Sanket Ghawali]

Dear gmx user

I am performing a MD simulation of peptides in sds for 100ns. After the
completion of my production I am unable to remove the periodic boundary
condition.
I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does
the periodic boundary condition affect my eccentricity result ?
Is it necessary first to remove the pbc effect and then calculate
Eccentricity.
Also does the high eccentricity value obtained after 100ns tell me that the
micelle is distorted and the peptide has some activity?

Thank you.
Sanket