[gmx-users] Perturbation Thermodynamic Integration

Dan Gil dan.gil9973 at gmail.com
Tue May 16 01:15:48 CEST 2017


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

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.

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,


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