[gmx-users] Question about Thermodynamic Integration

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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