[gmx-users] RE: Converting from AMBER to GROMACS

[Michel Cuendet]

Hi Jordi,

> The objective is to continue the simulation in the restart point, in 
> order
> to compare the trajectories obtained with AMBER and GROMACS.

Even if the two programs were computing perfectly correctly ;-) you 
would see your velocites diverge very soon. This happens even when 
comparing the same program on different architectures. This is well 
known, and comes from the chaotic nature of MD. On an other hand, 
average values should be comparable, but you don't need velocities for 
that.

Michel