[gmx-users] Perturbation Thermodynamic Integration

[Mark Abraham]

Hi,

Yes that looks like it is the envelope of the new warning. What does grompp
from 2016.3 report?

(Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
reject that method immediately unless there was evidence that it worked
well for a range of observables, and was consistent with other practice for
that force field. If there is such evidence, for my information, what model
/ force field does it like that?)

Mark

On Tue, May 16, 2017 at 3:30 PM 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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