[gmx-users] Free energy on GPU?

Justin Lemkul jalemkul at vt.edu
Thu Apr 18 20:43:43 CEST 2013

On 4/18/13 2:30 PM, Олег Титов wrote:
> Dear all.
> I'm trying to estimate relative solvation enegry of brombenzene (relative
> to benzene) via thermodynamic integration. Can I perform such calculation
> in GROMACS with GPU acceleration?
> As I currently understand to make use of GPU one need to use Verlet cutoff
> scheme. When I do so with pme electrostatics everything works fine until
> free energy calculation stage. Something strange happens there: the
> temperature of the system increases with increase of lambda value with no
> respect to thermostat (300 at lambda = 0.0 -> 500 at lambda = 1.0).
> Interesting fact that with reaction-field electrostatics everything seemed
> to work fine but now I cannot be sure that these results are reliable.
> As I understood from manual there is some issue with Verlet cutoff scheme
> and free energy calculations. Can I perform TI calculation in GROMACS with
> GPU acceleration or should I use group cutoffs and forget about GPU?

As far as I am aware, free energy calculations are not supported on GPU.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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