|From:||Michał Kański <michal.kanski@...2460...>|
|Date:||Fri, 17 Nov 2017 13:27:18 +0000|
Some useful links can be found here: http://lammps.sandia.gov/prepost.html
Personally, I would recommend VMD (http://www.ks.uiuc.edu/Research/vmd/) and TopoTools plugin (https://sites.google.com/site/akohlmey/software/topotools)
for converting pdb to lammps charge format.
From: Nnanna Ukoji <nukoji@...7190...>
Sent: Friday, November 17, 2017 1:50:46 PM
To: Michał Kański
Subject: Re: [lammps-users] WARNING: Fix qeq/reax CG convergence failed after 200 iterations at 1 step and ERROR on proc 0: Non-numeric atom coords - simulation unstable
Thank you for the quick response, It is indeed helpful. I just changed the data file to one of the data files in the example directory and it ran perfectly without warning or error.Please how can I generate a good data file for my system.
I used packmol to solvate the ethylene carbonate and lithium hexafluorophosphate which generated a .pdb file I viewed with VNL. I tried to save the solvate as a lammps data but VNL could only save it as atomic atom_style data with the charge (q) column missing, while I am using charge atom_style for my simulation.Is there a better means I can generate a data file compatible with charge atom_style for my system.?
On 17 November 2017 at 13:17, Michał Kański <michal.kanski@...2460...> wrote: