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.
Mark
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