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

[friendli]

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 about the hydrogens, do I need one or two dummy(DUM) atoms?
 
a), DUM <-> H ; H(of OH) <-> H(of NH2)
b), DUM <-> H(of NH2); DUM <-> H(of NH2); H(of OH) to DUM
a) or b) should I use?

2, I need to provide the coordinates for the dummy atoms in the .gro 
file(Asp), right? since otherwise the # of atoms in .top and .gro will 
mismatch.

3, from the tutorial(methane) I read, the masses of the dummy atom keeps 
like real atom and the C6 and C12 changes to zero in [atomtypes] to 
vanish the nonbonded interactions.  How to deal with the bonds and the 
charges for dummy atoms? bonded interactions?

I think I am a bit confused by the definition of the dummy atom.  I 
understanding is a dummy atom is a atoms with same mass but no 
interaction with all other atoms. Is that right?


thanks for help and suggestions are appreciate.

QL