[gmx-users] 1-4 Interactions

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Oct 19 15:35:20 CEST 2006

Did you remember to use pbc=xyz in your mdp file? It appears that you  
have a molecule broken between P8 and C13 of residue (dpc molecule)  
19. While dppc128.pdb has a pbc-broken residue 19, P8 and C13 should  
still be on the same side of the boundary (dppc_npat.pdb and  
dppc64.pdb have the entire molecule for DPC residue 19 in the same  

I haven't used dppc myself, but the files look good. Send some more  
info about your setup if you alreaady used pbc=full and the comments  
from Mark and Tsjerk don't lead to a solution. Also, pls check to see  
if you get any error/warning messages prior to the one that you have  

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