[Pw_forum] QE for aqueous solution?

[Giuseppe Mattioli]

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
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>


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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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