[gmx-users] box size changed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 1 00:42:17 CET 2007

Nancy Deng wrote:
> Dear All,
> I am a very beginner of Gromacs and currently trying to run two small 
> molecule (35 atoms) MD studies, one with water and the other without 
> water (skip the "genbox" step).
> Surprisingly, the box size of the system containing only small molecule 
> (without water) kept shrink till the program crashed with the error of 
> "one of the box vector has become shorter than twice the cut-off length".
> However, the other system (water + small molecule) behave just opposite, 
> i.e. the box size kept increased...
> So, I am wondering whether you have any idear how to fix this??? Whether 
> Gromacs is the right tool to sample small molecule conformational space.

This is a bit like telling us you were going to drive somewhere in 
America starting from Philadelphia. When you took the red car you ended 
up in New York, and when you took the yellow car you found yourself in 
Detroit. Apparently you didn't want to end up in either place, but you 
haven't told us where you're trying to go or how you're trying to get there.


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