[gmx-users] xx of the xxxx bonded interactions couldn't be calculated

Badamkhatan bdmkhtn at yahoo.com
Fri Jun 7 04:00:07 CEST 2013

Dear GMX-users

Recently i got this error and note from my MD2 simulation. I'm solvating
1-octanol to 1-octanol and calculating free energy differences. This is the
last step of my calculation and previous steps are looking fine. Basically i
followed Justin's free energy tutorial. 
Here is 
 A list of missing interactions:
        LJC Pairs NB of    210 missing      1
          exclusions of  25308 missing      1

Molecule type '1-octanol'
the first 10 missing interactions, except for exclusions:
        LJC Pairs NB atoms    3   25           global     3    25

Fatal error: 
2 of the 57736 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance (1
nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

Please help me and suggest any idea to solve this problem?

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