[gmx-developers] Loss of performance using Free Energy calculations in Gromacs-4.6.x

apratim87 apratim87 at gmail.com
Thu Jun 20 04:02:32 CEST 2013

I have been performing free energy perturbations with gromacs 4.6.2. 

The system contains 3246 atoms with 180 atoms belonging to the peptide. My
state B contains a scaled hamiltonian for the peptide i.e. the bonded and
nonbonded interaction parameters are scaled by a certain factor lambda. 

The pertinent entries in the .mdp files are: 

free-energy         = yes
init-lambda-state   =  3
coul-lambdas        = 0.34
vdw-lambdas         = 0.34
bonded-lambdas      = 0.34

I am getting a performance of 2.5 ns/day using a single core. However, if
free-energy is set to no, it results in 15ns/day. Can someone explain this
loss of performance using free energy calculations? 

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