[gmx-users] Perturbation Thermodynamic Integration

Dan Gil dan.gil9973 at gmail.com
Tue May 16 16:28:12 CEST 2017 

Thank you for the advice on the cut-off schemes and PME methods.

What is the physical meaning of a non-interacting final state
> that has different masses from the initial state?


These free energy options was just from me trying to figure out why mass
has any contributions at all. I am going from molecule A to B described in
the topology. In the actual simulations, I am planning on using this:
vdw_lambdas              = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
coul_lambdas             = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
bonded_lambdas           = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
restraint_lambdas        = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
mass_lambdas             = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

To get the solvation free energy difference between molecule A and B.

You'd need the latest grompp, as I've mentioned twice.


Sorry, I wasn't sure if I had the right version of grompp or not. I am
seeing if I can download the newest version of Gromacs to check.

On Tue, May 16, 2017 at 10:10 AM, Hannes Loeffler <
Hannes.Loeffler at stfc.ac.uk> wrote:

> 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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