[gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

Hello,

The last thread was getting too big, and the conversation evolved to a
topic different from my original question, so I decided to start a new
thread.

We were discussing thermodynamic integration, and why the mass_lambdas
would have any contribution to the derivative of the Hamiltonian.

I found a source (link below) which derives the Gibbs free energy change as
a function of lambda. I learned that the mass contribution is often assumed
to be small and negligible, given that the mass difference between the two
lambda states are small.
http://www.tandfonline.com/doi/abs/10.1080/00268970600893060

I think that the mass of the two lambda states that equation (14) is
referring to is the total mass (mass of solvent plus solute). My system is
1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder if I
am getting nonzero mass contributions (in my dhdl.xvg output) because of
finite-size effects? Would completely neglecting the mass contributions be
acceptable? Does doing this technically change the system to one that is 1
solute and an infinite number of solvent molecules where the mass
contributions limit is zero?

Best Regards,

Dan