[gmx-users] box size changed

Nancy Deng jdeng at adrik.bchs.uh.edu
Thu Mar 1 00:01:59 CET 2007

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.

I desperatedly need your advice and appreciate your any input!!!



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