[gmx-users] System is exploding

[David van der Spoel]

abhigna polavarapu wrote:
> 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
> abhigna
> 
> 
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your structure is bad.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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