[gmx-users] position and velocity in traj file & Verlet algorithm in GROMACS 3.3

[Mark Abraham]

Jianwei Wang wrote:
> Two questions:
> 
> (1) What are the positions and velocities stored in trajectory files by
> gmx3.3? I know the positions must be at current time (at time t), but how
> about velocities? are they at t-0.5*dt, t+0.5*dt or estimated at time t? If
> gmx3.3 uses leap-frog form of verlet, velocites at time t are not available
> or have to be estimated. 

If the velocities at time t are not being used, then I doubt gromacs 
computes their estimates - you can interpolate it yourself using the 
forces positions and neighbouring velocities, of course. Thus I'd expect 
the velocities in trajectory files to be at t-0.5*dt

> (2) Is the velocity verlet available? If gmx3.3 implements it, how to turn
> on velocity version of Verlet? Thanks a lot!

How about you search the manual for this?

Mark