Re: [gmx-users] set up topology in free energy calculations

QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will "diffuse" away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first

[gmx-users] set up topology in free energy calculations

Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O <-> N. What ab