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 <sheka...@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 <sheka...@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 <sheka...@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.matti...@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 <sheka...@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.an...@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@pwscf.org >>>> >> http://pwscf.org/mailman/listinfo/pw_forum >>>> >> >>>> >>>> >>>> -- >>>> ******************************************************** >>>> - 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.matti...@ism.cnr.it> >>>> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ >>>> ResearcherID: F-6308-2012 >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum@pwscf.org >>>> http://pwscf.org/mailman/listinfo/pw_forum >>>> >>> >>> >> >
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