[gmx-users] Question about Thermodynamic Integration

Justin Lemkul jalemkul at vt.edu
Wed Aug 8 20:35:53 CEST 2012

On 8/8/12 11:25 AM, Asaf Farhi wrote:
> Dear Justin
> Thank you very much for the reply.
> I want to understand how to calculate binding free energy difference of both molecules to another molecule.
> So do I have to use dummy atoms, meaning that there won't other forces besides the bonding term?
> I'll look at the examples.

Yes, bonded terms can and will be different. Start with a very simple example, 
like methane to ethane, before diving into your more complex system.  Follow the 
logic in the example in section 5.7.4 in creating your topology.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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