[gmx-users] Question about Thermodynamic Integration
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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