[gmx-users] A question about simulating a box of ethane in GROMACS

[Mark Abraham]

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