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
