[gmx-users] shell again

[Erik Lindahl]

Dmitry Kovalsky wrote:

>Hi there, 
>
>Tracing back a problem with option -shell ( Vol 1 #412) in genbox programm
>I have found out that depending on the shell value I get different results.
>
>I have used tried 0.3. and 0.15 nm shell and got very quickly (1 ns) two 
>distinct resulted conformations. 
>  
>
MD is a chaotic process, so when you have a different number of 
particles or different velocities there will
always be minor differences in the trajectories the atoms undergo. For 
every step, this will spread slightly,
so after a nanosecond or so it is quite reasonable that the two systems 
have diverged completely in phasespace.

Cheers,

Erik