[gmx-users] query on Free energy perturbation

[Justin A. Lemkul]

Sanku M wrote:
> Hi,
>   I was planning to use Thermodynamic integration to calculate solvation 
> free energy of a molecule in a solvent. I was following Justin Lemkul's 
> online tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
>  
> . I found that 
>    a) a sd integrator is used in stead of usual md integrator ( 
> Leap-Frog integrator). I was wondering whether is it a specific 
> recommendation for thermodynamic integration to use stochastic integrator ?

It's simply a more accurate integrator for sensitive quantities for which 
solvent viscosity may be important.  It also controls temperature via the 
Langevin method, which produces a proper canonical ensemble.

>   b) I also found  DispCorr = EnerPres was also used to Apply long range 
> dispersion corrections for Energy and Pressure . Is it also a 
> recommendation to use with thermodyanmic integration technique ?

Dispersion correction is necessary when plain cutoffs are employed for 
quantities that are sensitive to such truncation artifacts.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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