[Pw_forum] QE for aqueous solution?

Sat May 6 10:47:38 CEST 2017

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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