On 7/09/2011 5:23 AM, Phil (Yang) Song wrote:
Hi,
Thank everyone for your suggestions.
I have tried to put less molecule in a small box and find this works!
Eventually I have solve the problem by using a larger initial box size
for the random generated position and orientation. It seemed that the
overall interaction of OPLS-AA between ethanes is attractive rather
than repulsive, which leads to atomic clashes...
Random positions and orientations are different from non-clashing random
positions and orientations. If your random generation takes account of
inter-molecular forces, then it's not random, and won't lead to atomic
clashes. So there is something missing or wrong about your description.
Mark
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