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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