[[email protected]...: MOLECULAR DYNAMICS HELP]

Dear Majid,

I hope you don't mind if I reply to the LAMMPS mailing list. Other
people may help or learn, and my work will be promoted.

It would be interesting to see the LJ plot zoomed in the minimum
energy area. Check the LAMMPS documentation on "units".

I did not divide the box into 146 parts. I used packmol. Examples were
very helpful. Try to increase minimum distance between atoms - some of
them seems to form "bonds" on your image.

You pair_coeff looks ok, but make sure you are getting correct LJ
plots (check units).

I used full atom style, not hybrid, with rcut=11Angstroms.

-Bohumir
http://www.cavs.msstate.edu/information.php?eid=69

1215.png

12121.png

Dear Bohumir

thanks for your advice

You Have proposed to increase minimum distance between atoms in packmol. We use tolerance in the input fille to specify the distance tolerance (for all of generated atoms), but I want to increase the minimum distance between Na & Cl ions (not all of my atoms), what is your idea to achieve this goal?

Best regard

Majid Rezaei

Dear Majid,

I have never tried to specify multiple tolerances in packmol - I don't
know how to do it.
I used only one tolerance.

Examples on packmol website were useful.

-Bohumir