[gmx-users] query on Free energy perturbation

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 30 22:00:37 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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