[gmx-users] Question about Thermodynamic Integration

Asaf Farhi asaf.farhi at weizmann.ac.il
Thu Aug 9 07:59:38 CEST 2012

Dear Justin

Thank you very much.
I really appreciate it.

Best regards,
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, August 08, 2012 9:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Question about Thermodynamic Integration

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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