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
--
========================================
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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