[gmx-developers] No WHITE nodes found error

Carsten Kutzner ckutzne at gwdg.de
Thu Sep 11 16:53:50 CEST 2008


I am having some trouble with one MD system here. I am using
today's CVS gromacs for a (big) system which runs fine with
older CVS versions. I think the problem is related to the new
molecular topology code. The error message I get is

Program mdrun, VERSION 4.0_beta1
Source code file: mshift.c, line: 575

Fatal error:
No WHITE nodes found while nW=3369


The problem seems to me that in do_pbc_first_mtop (l. 305 of md.c)
at one iteration of the loop a graph with g->nnodes = 0 is created
by mk_graph_ilist (while at the same time g->nbound=nW=3369 in mk_mshift).
A bit later in  the routine first_colour the loop

for(i=fC; (i<g->nnodes); i++)

is not executed, since both fC and nnodes are 0, therefore the
first_color routine returns -1, triggering the gmx_fatal.

Thanks for any hints.


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