[gmx-developers] insertion-deletion

Jason DeJoannis jdejoan at emory.edu
Thu Apr 22 22:36:42 CEST 2004

Dear All,

Consider a lennard-jones fluid. I want to perform insertions
and deletions provided

            1 < n < n0

where n  is the number of atoms
      n0 is the number of atoms in the starting config

All I do is change top->atoms.nr and all the other measures of
the number of atoms (i.e. inside mdatoms,top->atoms,top->blocks,nsb).
Directly afterwards a new neighbor search is performed.

Unfortunately after a dozen or so steps, one or more of the forces
becomes "nan". Right now I am running in serial mode with 10 atoms to
keep things simple.

Any idea what is killing my forces?

Jason de Joannis, Ph.D.
Chemistry Department, Emory University
1515 Pierce Dr. NE, Atlanta, GA 30322
Phone: (404) 712-2983
Email: jdejoan at emory.edu

More information about the gromacs.org_gmx-developers mailing list