[[email protected]: MOLECULAR DYNAMICS HELP]

Dear Majid,

thanks for your interest in our IJTAMM paper on the "Effects of
Surface Charge Density and Distribution on the Nanochannel
Electro-osmotic Flow". Unless you already did, you can also download a
preprint version:

  http://www.cavs.msstate.edu/publications/docs/2011/10/9189main.pdf

Could LAMMPS team please add the paper

  http://dx.doi.org/10.1504/IJTAMM.2011.043537

to the LAMMPS publication list?

Steps of the simulation are also described in the presentation I made
on that work at the APS DFD meeting:

  http://www.cavs.msstate.edu/publications/docs/2010/09/8089apsdfd2010_01.pdf

and resulting plots were summarized at the LAMMPS workshop presentation:

  http://lammps.sandia.gov/workshops/Aug11/Jelinek/Bohumir_e-osm_LAMMPS2011.pdf

Since the initial energy before relaxation is very large:

---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 35586048822.4488 KinEng = 6632.6004 Temp = 300.0000
PotEng = 35586042189.8483 E_bond = 3502.9189 E_angle = 892.4212
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 35586026063.1936
E_coul = 1460.6589 E_long = 10270.6557 Press = 94763360047.7623

some atoms are likely too close - as other experts pointed out too. On
the other side, if atoms move too far after relaxation, make sure that
they are packed densely enough (i.e. that there are no large void
spaces between them). If ions and water molecules are positioned
randomly and densely enough, they should not relax to the wall - that
is too much movement from relaxation and one possibly atoms are not
packed densely enough. I used Packmol to generate initial positions.

You also need to check if the description of the potential is correct.
Try to make an LJ plots as the one on page 23 of my APS DFD
presentation. SPC/E model of water is described in LAMMPS
documentation:
  http://lammps.sandia.gov/doc/Section_howto.html#howto_9

There is a lot of hard work ahead of you. I wish you to enjoy the fruits of it.

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