hi. i'm beginner in martini simulation.
i do tutorial's protein that is in this address:
www.cgmartini.nl/index.php/tutorials-gen...ion/proteins#martini
and reach to production run step (7 step).when i look at the "dynamic.gro" file, with vmd, i see peptide at the corner of box.what is its reason? do i have to do equilibration step on "dynamic.gro" file?
thank you.