Hello Gromacs community, 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?
Thank you in advance for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering
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