[gmx-users] System is exploding

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 20 20:07:09 CET 2007

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
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
search the archives.
your structure is bad.

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

More information about the gromacs.org_gmx-users mailing list