[gmx-users] Alchemical Tranfermation

[Ilya Chorny]

Hi

I have a strange bug in my system. I am trying to do an alchemical
transformation. I'm doing it using a single topology. I need to use soft
core potentials because I am introducing and taking away and atom but
when I use the soft core potentials one of my torsions flips and causes
an equatorial group to flip to an axial position. Is there any way for
me to overcome this problem?

Thanks

Ilya