[gmx-users] Perturbation Thermodynamic Integration

[Dan Gil]

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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