Dear Sanket,
Removing periodicity is difficult if SDS molecules transiently leave the
micelle and return after having moved one or more unit cells. You might want to
try using gmx clustsize to generate snapshots along the trajectory and use
trjconv on them to put all molecules in the same unit
Hi Sanket,
You probably want the clustering routine of trjconv. And then calculate the
principal axes of the micelle. The instantaneous value does not mean much,
but a an average non-zero eccentricity would suggest with a greater extent
than without peptide would suggest an effect. Note that you d
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 eccentricit
