[gmx-users] Question about Thermodynamic Integration

Justin Lemkul jalemkul at vt.edu
Wed Aug 8 17:07:38 CEST 2012

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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