[gmx-users] Question about Thermodynamic Integration

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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