[gmx-users] Defining a new molecule type

[Ali Khodayari]

Dear Users,

 

I am trying to use the free energy code to partially shut down the
non-bonded interactions in part of my system.

I only want to decouple interaction in some part of my system, I have put
all the desired residues in groups in the index file. What should I indicate
for the couple_moltype line? As the system consists of large number of atoms
in the same molecule type. Introducing a new molecule type is not possible
because the atoms are connected chain-wise and I want to decouple the
interactions in the middle of the chain.

Thank you for your responses.

Regards,

Ali