[gmx-users] free energy

[Andrei Neamtu]

Hello,

I tried for the first time the free energy perturbation code and I am a little confused. I am convinced I make a mistake somewhere but I cannot see where is it.
I simulate a polymer system and I want some atoms in the simulation box to "dissapear"; this means to set the vdW, Coulomb and bonded parameters to 0.0 in the state B for these atoms (Is this right?).
When I use the topology .itp file without specifying any parameters for state B, everything goes well, but when I introduce the state B parameters for the atoms I want to "dissapear" the simulations crash EVEN IF I "SET FREE_ENERGY = no" in the .mdp file. The grompp program shouldn't ignore the state B parameters in this case and use the "normal" ones (without any modification during the course of the simulation)?
Anyway, as I said, even if I set the free_energy = no in the .mdp file the simulation results differ from that obtained with a .mdp file without any state B parameters specified and it crashes (using the same starting structure)!
I don't know where I go wrong in setting the parameters for free energy.
I will be very grateful if anyone can help me with an advice concerning this problem.
Thank you very much,
Andrei
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