[gmx-users] RMSD VS. parallel simulation

[Mark Abraham]

DeChang Li wrote:
> Dear all,
> 
>   I used Gromacs-3.3.1 to simulate a small protein in water.
> I have used 2 and 16 CPUs to do the simulation respectively. But
> I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs
> simulation and 0.20 nm in the 16 CPUs one. Are these differences
> reasonable?

MD allows you to observe an ensemble (usually at or approaching 
equilibrium) over time. Any single point of that time isn't any more 
significant than any other.  So you should expect any pair of points in 
different simulations (which had their velocities generated with 
different random numbers, right?) to generally give different values for 
observables, and for that not to mean anything much. Distributions of 
observables over long enough periods of time should be the same, however.

>   In the 16 CPUs simulation, the RMSD of protein at t=0 was about
> 0.1 nm, why not equal to zero? I used the initial structure for the
> least squares fit.

If you've done an equilibration or EM, the structure can have changed 
during that.

Mark