[Pw_forum] QE for aqueous solution?

Sat May 6 11:33:48 CEST 2017

Dear Mattioli,
You are right and I strongly agree with you DFT is capable of providing a
universally-agreed on framework to deal with the temperature dependence of
liquid water via the CPMD technique. What I am trying to say is that
simulating an aqueous solution by a triclinic Bravais lattice--as is
demonstrated in the example--is not but a simple, imprecise approximation.
And no one can provide a better, more precise picture within QE.

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 1:27 PM, ashkan shekaari <shekaari at gmail.com> wrote:

> 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)
>>>>     Tel + 39 06 90672836 - Fax +39 06 90672316
>>>>     E-mail: <giuseppe.mattioli at ism.cnr.it>
>>>>     http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
>>>>     ResearcherID: F-6308-2012
>>>>
>>>>
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>>>
>>>
>>
>
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