It says the system not charge neutral. As of now I do not know whether lammps can simulate systems when the net charge is not neutral.
Arun
Thanks, Arun!
I found this previous post, based on which I assumed that by using the Ewald summation, there is a uniform background charge to correct the energy in cases of non-neutral systems:
http://sourceforge.net/p/lammps/mailman/message/32264332/
I have used the dielectric command to set the global dielectric constant.
The potential energy after minimization is of the same (way too big) magnitude in all cases that are not working (case [4] and [5]), whereas I have Epot=7557.068 after minimization for the working case [3] for example. All other inputs (e.g. data file, force field parameters, simulation setup) stay the same throughout the different cases, and I am really only modifying the “pair_style” and “special_bonds” commands.
I definitely agree that Epot is way too large in cases [4] and [5], I just cannot see a reason why…
Thanks, Arun!
I found this previous post, based on which I assumed that by using the
Ewald summation, there is a uniform background charge to correct the energy
in cases of non-neutral systems:
this compensation happens, but that doesn't mean it is a good idea to have
as highly charged a system as you have. you are basically simulating a
crystal that would instantly produce a massive explosion. this background
change compensation is acceptable for total system charges of 1-2 at the
most. it is almost always better to make a system neutral.
I have used the dielectric command to set the global dielectric constant.
by what justification? for normal all-atom simulation it has to be 1.
The potential energy after minimization is of the same (way too big)
magnitude in all cases that are not working (case [4] and [5]), whereas I
have Epot=7557.068 after minimization for the working case [3] for example.
All other inputs (e.g. data file, force field parameters, simulation setup)
stay the same throughout the different cases, and I am really only
modifying the "pair_style" and "special_bonds" commands.I definitely agree that Epot is way too large in cases [4] and [5], I just
cannot see a reason why...
your input is bad in places where you just assume that it is correct. it
is very difficult to debug this from the outside.
break down your simulation into small parts and test and check each part by
itself. that is the only way to go.
axel.
Thanks a lot for all the helpful comments, Axel!
I’ll go ahead and break down the simulation…
Best,
Mia