[gmx-users] Perturbation Thermodynamic Integration
Dan Gil
dan.gil9973 at gmail.com
Tue May 16 15:53:56 CEST 2017
Hi,
The latest version of Gromacs I have is 5.1. Using this version, grompp
produces no warnings or errors.
I am using OPLS-AA, and I didn't have any issues with it thus far. I
inherited this research project though 3 years ago. Is there something you
think I should look at with scrutiny?
On Tue, May 16, 2017 at 9:42 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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