[gmx-users] Free energy perturbation protocol

[bmbbl at leeds.ac.uk]

Hi there,

I want to confirm my protocol of free energy difference calculation using FEP
with GROMACS.

A-B and A-B' complex

1. Full MD on A-B complex. input 1.tpr; output: 1.xtc, 1.gro
2. perturbation topology indicated as: B --> B' names as newtp.itp
    grompp -f FEP.mdp -o 2.tpr -c 1.gro -p newtp.itp
3. mdrun -c 1.tpr -rerun 1.xtc -o AB.edr
   mdrun -c 2.tpr -rerun 1.xtc -o AB'.edr
4. g_energy -f AB.edr -f2 AB'.edr -fee -o FE.xvg

My question is on step 2 and 3. Do I have to run full MD using 2.tpr and 1.gro
to generate a new 2.xtc file or I can simply apply 1.xtc to the -rerun?

Thanks for any hint!

Best,
Binbin