[gmx-users] total charge of the system
Daniel Adriano Silva M
dadriano at gmail.com
Fri Jul 11 03:33:38 CEST 2008
If the "real charge" of your system is not zero and you are using PME, then
PME code will take account for any non-zero charge on the system and
neutralize it with an uniform background charge (
If your system is composed by a protein, then try first to check the charge
for every residue (maybe you found some aminoacid with a not integral
Please note that several times if your charge is very close to an integer,
this warning is generated as consequence of the " summation of many floating
point numbers", check this link:
However, your error is on the 3rd digit (by a magnitude of .004), on my
experience gromacs "round errors" are very close to the integer (e.g. Sytem
Charge = .9999998 or 1.000002), then I recommend you to take a look on your
2008/7/10 serdar durdagi <durdagis at yahoo.de>:
> Dear all,
> In one of my simulations, total charge of the system is a noninteger number
> (like +15.996). I neutralized it with 16 chlorine atoms. I am using periodic
> boundary conditions. If I use the charge as it is, is it means infinite
> negative total charge on the system?
> Actually, when I check the simulation output parameters, it seems every
> thing okay..I am just curious if it's some thing wrong..
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