That really depends how you define the various regions for your molecule pair.
If you define all atoms to be "softcore", and thus run "fully" dual-topology, you will only get TI gradients for non-bonded and electrostatic terms (with the environment. I am not sure if there is an option to also include the intra-contributions). But be aware that your end-points will be ghost molecules and you may have to work with restraints if there is no covalent bond between the TI region and other parts of your system.
You can also define only a subset as softcore which implies that the rest will be computed in a single-topology fashion, i.e. you will also get gradients for all bonded terms not including any softcore atoms. This will require a one-to-one mapping of atoms and will require a certain similarity between the atoms. In practice you will probably only mutate a few atoms (atom types).
Cheers,
Hannes.
________________________________________
From: wangmt [wangmt.itcs.ecnu.edu.cn]
Sent: 29 December 2014 14:21
To: amber.ambermd.org
Subject: [AMBER] TI calculation using pmemd
dear all
I want to calculate the free energy change in converting one small
molecule (A) to another (B) in solution using TI approach by pmemd.
But I am not sure whether the change of internal energies (such as bond,
angle, and dihedral energies) are included in the besides VDW and
electrostatic energies, because molecule A and B has different number of
atoms.
Could you please give me some guidance? Thanks a lot.
Meiting,
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Received on Mon Dec 29 2014 - 09:30:02 PST
