[gmx-users] counterions

John Kerrigan kerrigje at umdnj.edu
Thu Jun 5 20:53:01 CEST 2003


Use genion.  Solvate your system first; create a tpr file then run genion.
genion will replace water molecules by the # of ions you specify and
create a new gro file. You
will need to edit your topology file

add #include "ions.itp"
add a line under [molecules] for the ion(s) and subtract the appropriate #
from SOL.

Remember to check ions.itp to insure you are using the proper name of the
ion for the forcefield you are using in gromacs (the ions are listed by
forcefield in ions.itp).

Hope this helps.



John E. Kerrigan, Ph.D.
Dept. of Pharmacology
Robert Wood Johnson Medical School, UMDNJ
675 Hoes Lane
Piscataway, NJ 08854 USA

(732) 235-4473 phone
(732) 235-5252 FAX

More information about the gromacs.org_gmx-users mailing list