[gmx-users] Question about Thermodynamic Integration
jalemkul at vt.edu
Wed Aug 8 12:05:21 CEST 2012
On 8/8/12 3:11 AM, Asaf Farhi wrote:
> Dear Gromacs users
> Hi. I wanted to ask about the use of Thermodynamic Integration.
> If the two compared molecules have a different number of atoms (e.g Theophylline and Methylxanithe) what should I do in order to simulate it well (it's written that you have to have the same number of atoms)?
If by "comparing molecules" you mean you are evaluating differences in, e.g.,
hydration free energy, there is no such requirement. What I believe you are
thinking of is a FEP transformation between different species, an in silico
mutation process. In that case, one would use dummy atoms that are transformed
into real interacting species over the course of the lambda-dependent
transformation. In the case of TI, no such requirement exists.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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