[Pw_forum] QE for aqueous solution?

Sat May 6 10:57:38 CEST 2017

To the best of my knowledge, David could examine only the atomic structure
of the solute using high-performance computer clusters supposing that the
solute is made of not a large number of atoms and he has to write on his
own several codes in order to obtain the temperature dependence of some
phase transition indicators such as mean-square displacements and the
Lindemann index.

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 1:17 PM, ashkan shekaari <shekaari at gmail.com> wrote:

> Actually, I have recently published a paper on melting behavior of some
> graphene quantum dots containing 6 and 10 atoms, but I had to write on my
> own more than 800 program lines in bash and fortran for such small-sized
> structures to get my desired results. And it is based on such an experience
> that I believe QE is not that sophisticated in DFMD calculations of large,
> non-solid, molecular structures. Even if you are a highly-experienced
> programmer, you cannot get the desired results conclusively as the number
> of atoms increases to form a solution.
>
> 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 1:00 PM, ashkan shekaari <shekaari at gmail.com>
> wrote:
>
>> 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
>>>     CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>>>     v. Salaria Km 29,300 - C.P. 10
>>>     I 00015 - Monterotondo Stazione (RM)
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>>
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