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!!!
Thanks,
nancy
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