[gmx-users] Re to Berk Hess (pull code core dump)

Berk Hess gmx3 at hotmail.com
Thu Oct 14 14:19:39 CEST 2004

>The question is: how the bond lengths can just explode? to large 
>integration step? but I'm using a typical 2 fs time-step for a typical 
>united-atom system!
>Or it can be due to the readjustment of the distance between the two 
>reference groups, were the atoms can be to near and then the forces become 
>two strong and the Lincs algorithm can't adjust the distances to the 
>correct values. So this can be a problem with the methodology used for this 

My best guest is that when the molecule is close to the bilayer the pull 
makes the system too stiff, which causes the integration to fail.
Maybe you should switch to AFM pulling for calculating the PMF.


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