[Pw_forum] QE for aqueous solution?

[ashkan shekaari]

Dear Mattioli,

Water is not a crystal and therefore it cannot be treated as a
periodic structure.
The aforementioned example provides only a naive picture of water as an
aqueous compartment leading to a crude approximation of the given system as
well. Moreover, QE is not best suited for DFMD simulations of large,
nonperiodic, liquid systems.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:

>
> Dear David and Ashkan
>
> > You cannot simulate the system as periodic. You have to use a large super
> > cell with vacuum spaces along the three spatial directions. Moreover, you
> > can simulate the solution only via importing a large number of atomic
> > positions of the order of 25000 at least, which does not seem to be
> > feasible by QE even in case of using random generators unless you have a
> > supercomputer facility.
>
> This comments are misleading, if not wrong in some cases.
> First of all you can for sure perform ab initio molecular dynamics
> (aimd) simulations of a water solution in a periodic box, and you do
> not need a huge number of atoms. One of the cp.x examples provides
> starting points, see here
> /Your_Path_To_Espresso_6.1/Examples/CPV/example04
>
> >> Does anyone know of examples, benchmarks, or recommendations?  Would the
> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> >> about parameter settings for this application would be much appreciated
>
> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.
> They used to be old and well-tested vanderbilt ultrasoft
> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But
> if you are not familiar with this terminology (ultrasoft,
> norm-conserving, van, mt, rrkj, paw, ...) you should start with some
> tutorial on pseudopotentials, because you must be sure to use
> converged plane-wave and density cutoffs for a given set of
> pseudopotentials.
>
> There is a very large number of options that must be set in the cp.x
> input. I cannot review them here. But there are also tons of
> literature on aimd simulations of water solutions, and you will easily
> find something that will help to choice a lot of parameters (box
> dimensions, NVT, NVP, NVE dynamics, thermostats, ...)
>
> > Indeed, QE is not best suited for MD simulations and I strongly recommend
> > the gromacs package.
>
> Of course Ashkan might be right on a couple of points: if you have
> very big molecules weakly interacting with the solvent, and you are
> interested in the morphology of the solute only, then you have to
> perform very long md simulations and to use a large number of water
> molecules, and this might be costly and time-consuming if performed at
> an aimd level. If you want to study proton exchanges, reactions,
> dipole dynamics, ... you need aimd. You surely know whether your
> scientific task strictly requires aimd rather than model-potential md.
>
> HTH
> Giuseppe
>
> Quoting ashkan shekaari <shekaari at gmail.com>:
>
> > Indeed, QE is not best suited for MD simulations and I strongly recommend
> > the gromacs package.
>
> > You cannot simulate the system as periodic. You have to use a large super
> > cell with vacuum spaces along the three spatial directions. Moreover, you
> > can simulate the solution only via importing a large number of atomic
> > positions of the order of 25000 at least, which does not seem to be
> > feasible by QE even in case of using random generators unless you have a
> > supercomputer facility.
> >
> > On May 6, 2017 9:09 AM, "D J Anick" <david.anick at rcn.com> wrote:
> >
> >> Hello plane wavers,
> >>
> >> I am interested in using QE for a molecular dynamics simulation of an
> >> aqueous solution containing a solute, modeling it as a 3-D periodic
> cell.
> >> Principal questions would be about solvation shell geometries,
> distribution
> >> of configurations adopted by the solute, and H-bond duration /
> stability.
> >>
> >> Does anyone know of examples, benchmarks, or recommendations?  Would the
> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> >> about parameter settings for this application would be much appreciated.
> >>
> >> Thank you in advance,
> >> David Anick
> >> david.anick###rcn.com
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> >>
>
>
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>     Giuseppe Mattioli
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