LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] optimization of structure
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] optimization of structure

From: Steve Plimpton <sjplimp@...24...>
Date: Thu, 12 Oct 2017 07:16:32 -0600

There is no simple answer to this Q.  If LAMMPS
can minimize and then run dynamics without
things blowing up, then the bad initial structure
is not an issue numerically.  But whether
the bad structure locks in some geometry
that is bad for your subsequent analysis
is not a LAMMPS Q.


On Wed, Oct 4, 2017 at 7:23 AM, Hossein Geraili <geraili.hsn@...24...> wrote:
Dear Lammps users,
Is it really important that the .pdb file(input of Packmol for creating Lammps datafile through Topotools) be optimized properly? I mean,  if it has like 20% error in energy compared to the optimized structure on the same basis set in reference, the Lammps simulation will not be correct? Or Lammps minimization will do this work and there is no difference between the correctly optimized .pdb and the .pdb with the error. I am getting parameters and charges from the article, so I think basically the initial structure is just some initial coordination of atoms for parameters to be implemented, am I right?
I am simulating an ion pair, so maybe the distance between oppositely charged ions should be correctly optimized in the first place. yes?
Best regards

Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.

Sent with Mailtrack

Check out the vibrant tech community on one of the world's most
engaging tech sites,!
lammps-users mailing list