[gmx-users] Question about Thermodynamic Integration

Asaf Farhi asaf.farhi at weizmann.ac.il
Wed Aug 8 17:25:12 CEST 2012

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.

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 6:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Question about Thermodynamic Integration

On 8/8/12 6:35 AM, Asaf Farhi wrote:
> Dear Justin
> Thank you very much for the reply.
> It's written in the manual:
> 5.7.4 Topologies for free energy calculations
> Free energy differences between two systems, A and B, can be calculated as described in sec. 3.12.
> Systems A and B are described by topologies consisting of the same number of molecules with
> the same number of atoms.

Perhaps you need to state for us more clearly what you're trying to do.  If you
want to transform theophylline into methylxanthine, then you have some work to
do in constructing dummy atoms that are transformed into real atoms over the
course of the transformation.  There are examples in the list archive in terms
of transforming one amino acid into another so I would suggest you search if
this is what you're after.

If you aim to simply calculate independent hydration energies (in two separate
systems), I don't see what the problem is.  Simple decoupling turns interaction
atoms into the same number of non-interacting sites or vice versa.



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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