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
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