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 < [email protected]> 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 <[email protected]>: > > > 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" <[email protected]> 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 > >> [email protected] > >> 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: <[email protected]> > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > ResearcherID: F-6308-2012 > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum >
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