[gmx-users] Perturbation Thermodynamic Integration

[Hannes Loeffler]

I have not really followed the previous email exchange but from this
mdp file I wonder what you are trying to achieve.  You seem to want to
decouple all atoms of your HEPT molecule (couple-moltype,
couple-intramol) from its environment but then you also change the
masses.  What is the physical meaning of a non-interacting final state
that has different masses from the initial state?  I believe the mass
contributions are supposed to cancel in a closed thermodynamic cycle
but what is the cycle you are simulating?


On Tue, 16 May 2017 09:30:08 -0400
Dan Gil <dan.gil9973 at gmail.com> wrote:

> Sorry, here is the mdp file:
> 
> ;Integration Method and Parameters
> integrator               = sd
> nsteps                   = 100000
> dt = 0.002
> nstenergy                = 1000
> nstlog                   = 5000
> 
> ;Output Control
> nstxout = 0
> nstvout = 0
> 
> ;Cutoff Schemes
> cutoff-scheme            = group
> rlist                    = 1.0
> vdw-type                 = cut-off
> rvdw                     = 2.0
> 
> ;Coulomb interactions
> coulombtype              = pme
> rcoulomb                 = 1.0
> fourierspacing           = 0.4
> 
> ;Constraints
> constraints              = all-bonds
> 
> ;Temperature coupling
> tcoupl                   = v-rescale
> tc-grps                  = system
> tau-t                    = 0.1
> ref-t                    = 300
> 
> ;Pressure coupling
> pcoupl = parrinello-rahman
> ref-p = 1.01325
> compressibility = 4.5e-5
> tau-p = 5
> 
> ;Free energy calculation
> free-energy              = yes
> init-lambda-state        = 8
> delta-lambda             = 0
> fep-lambdas              =
> calc-lambda-neighbors    = 1
> vdw_lambdas              = 0 0   0   0   0   0   0   0   0   0   0
> coul_lambdas             = 0 0   0   0   0   0   0   0   0   0   0
> bonded_lambdas           = 0 0   0   0   0   0   0   0   0   0   0
> restraint_lambdas        = 0 0   0   0   0   0   0   0   0   0   0
> mass_lambdas             = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
> couple-moltype           = HEPT
> couple-lambda0           = vdwq
> couple-lambda1           = none
> couple-intramol          = no
> nstdhdl                  = 10
> 
> 
> On Tue, May 16, 2017 at 1:02 AM, Mark Abraham
> <mark.j.abraham at gmail.com> wrote:
> 
> > 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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