[gmx-users] RE: General query regarding MD simulation

[Dr. Vitaly Chaban]

> 2. As suggested by a a person I know, I can do the charge calculation of
> the whole system including the Mg ion, water molecules and the residues.
> The explanation was that since GDP is in coordination to Mg ion, the
> effective charges would be different than on a GDP alone.


Yeah... and keep in mind that charge calculations are good only for
small systems (molecular fragments). The larger system you have, the
more ambiguous those calculated charges become. So it is not a panacea
to recalculate them for the whole protein, unfortunately.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark