Respected sir With regards
Thanks a lot for your great words of wisdom. I feel highly grateful. I'll be careful to take large super cell and thousands of time steps. Please sir, I have another query. I am trying to run MD simulations for gold nanotube which is periodic in x axis and has a circular ring of 12 atoms which is fixed and super cell is of 48 atoms. But after few hundred steps only this circular ring distorts turns octahedral types and after few more steps it turns curved like star but is continuos. However in x direction the tube remains intact and has not broken or deformed from anywhere. So, should I treat it as a structural deformation or instability or continue the MD runs further and with a more bigger super cell. Any further help is highly appreciated. Please guide me further . Thanks Pooja India On Mon, May 11, 2020, 1:32 AM Salvador Barraza-Lopez <[email protected]> wrote: > The answer is in the "dynamics.f" routine, where all MD algorithms are > written. > > The temperature you enter in your input is the "target" temperature. The > code moves atoms so that their kinetic energy is consistent (on average) > with your target temperature, but you are not to expect it to match it at > every MD step... the Nose thermostat takes/gives kinetic energy as the > calculation goes, precisely to achieve the target temperature. > > Your Nose Mass should not be too small, to actually let the system > explore a range of temperatures. > > Once you have sufficient MD steps, you can then discard many at the start > of the run (when thermalization is just being set up), and then get an > average temperature. In all my runs, I get the average temperature to be > within 1% of the target one, after tens of thousands of MD steps for good > averaging. > > Your supercell should also be large enough to get meaningful results. > > You should also read Nose papers on the subject. > > Going at it expecting certain numbers and without a grasp of theory could > be dangerous and not recommendable. > > ----------------------------------------- > Salvador Barraza-Lopez > Associate Professor of Physics > University of Arkansas > https://wordpressua.uark.edu/sbarraza/ > > ------------------------------ > *From:* [email protected] <[email protected]> on behalf of > pooja pu <[email protected]> > *Sent:* Saturday, May 9, 2020 4:31 AM > *To:* [email protected] <[email protected]> > *Subject:* [SIESTA-L] Abinitio MD simulations > > Respected all > > I'm new to MD simulations using siesta > There are different types of MD runs like nose, Verlet. Using nose however > temperature is changing in every step and not becoming constant up-to 2ps > while it is said calculation using nose thermostat are at constant > temperature ? How is thermal stability of a system checked using MD > simulations in siesta? > Please let me know. Any help and guidance would be highly appreciated. > Please if anyone knows the answer please help me. > > Thanks > > With regards > > Pooja kapoor > India > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
