[gmx-users] System is exploding

abhigna polavarapu abhignap at gmail.com
Tue Mar 20 19:57:21 CET 2007

I am running a 10ns simulation on a 42 mer peptide. I am doing this for
predicting the stability of the beta sheet. So I deleted a bond called the
lactame bond between two amino acids Lys and Asp. So if I just create
mutation  at any other position in the beta sheet the mdrun crashes with an
error saying that 1-4 interaction between the residues in Lys is greater
than the size of the box. Increase the table extension. This seems like
system is exploding. But if I mutate those two amino acids to Ala I am not
getting that error. So please help me with this. As I need to analyse lots
of mutations othen than mutation those two amino acids

Thank you
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