David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 23 08:47:04 CEST 2004
On Thu, 2004-04-22 at 22:36, Jason DeJoannis wrote:
> 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?
How about the lengths of the force arrays, coordinate arrays and son on?
> 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
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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