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Enhancing the performance of the free energy code - Redmine #742

Archive from user: Luca Bellucci

Dear all,
free energy perturbation (FEP) module of GROMACS 4.5 can be used to perform
Hamiltonian replica exchange molecular dynamics (H-REMD). The main modules that “drive”
H-REMD simulation are src/kernel/repl_ex.c and /src/gmxlib/nonbonded/ nb_free_energy.c
I tried to perform H-REMD decoupling a small peptide in
water. In this case I observed about a 40-50% reduction in speed.
When I tried to decouple water and peptide the performance loss is much more dramatic.
I posted my test files in:
https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1
This is a run for a dialanine peptide in a water box.
The cell side cubic box was 40 A.
The directory is organized as :
TEST\
topol.top
Run-00/confout.gro ; Equilibrated structure
Run-00/state.cp
MD-std/Commands ; commands to run the simulation , grompp and mdrun
MD-std/md.mdp
MD-FEP/Commands
MD-FEP/md.mdp
For more details in this issue see also gmx-users mailing list:
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060169.html

FEP code is bug free, but a this stage it is unusable to perform H-REMD
due to the low performance.

Free Energy Perturbation with Replica Exchange Molecular Dynamics offers
a powerful strategy to enhance the sampling of biological system, therefore
I would suggest to improve its efficiency.
Best regards
Luca

(from redmine: issue id 742, created on 2011-04-26 by gmxdefault)