Hello Gromacs community,<br><br>I am trying to simply decharge a part of large molecule. I know from the tutorial we can use 'couple-moltype' along with 'couple-lambda0', etc, but in this case I simply change the topology to state A and then I have state B written with no charges since I'm only doing a piece of the molecule. I have a free energy but it is only the free energy including interactions between the piece of the molecule and surrounding solvent. I see 'couple-intramol' is an option to have intramolecular interactions also decoupled but it requires a 'couple-moltype' to be set. Is there any way I can set that variable to simply a piece of a molecule? <br>
<br>Thank you in advance for your help.<br clear="all"><br>-- <br>Best regards,<br> <br>Fabian F. Casteblanco<br>Rutgers University --<br>Chemical Engineering<br>