[Pw_forum] QE for aqueous solution?

Sat May 6 10:51:18 CEST 2017

Dear Ashkan
I'm afraid I do not agree with you. Among many examples, I remember  
this now classical paper written by *very* skilled colleagues ;-)
The influence of temperature and density functional models in ab  
initio molecular dynamics simulation of liquid water. J VandeVondele,  
F Mohamed, M Krack, J Hutter, M Sprik, M Parrinello
The Journal of chemical physics 2005, 122, 014515.
That was performed by using the CPMD (periodic+plane  
waves+pseudopotentials) suite of programs, if I remember well (by  
heart, because I'm abroad and I cannot access literature now), O-O  
g(R) was converged and in agreement with measurements by using a not  
so big periodic box and a not so long (initial equilibration + ~10 ps)  
simulation time.
Maybe there are choices better than QE for this kind of ab initio  
simulation (CP2K? CPMD?), but I would not give it for granted...
Best
Giuseppe

Quoting ashkan shekaari <shekaari at gmail.com>:

> 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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-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
********************************************************

    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