[gmx-users] Perturbation Thermodynamic Integration

[Mark Abraham]

Hi,

What use are you making of constraints? Justin suggested sharing a full mdp
file, which I think may help. We discovered last year that you can get
equipartition failure for (IIRC) all-bonds constraints for moieties like
-CH2Cl, and latest grompp now detects this.

Mark

On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9973 at gmail.com> wrote:

> 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
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