On Sat, Apr 27, 2013, kurisaki wrote:
> I'm now trying to print out force information through MD run.
>
> First, I added "print command" to runmd.F90,
> Just before velocity is up-dated in "the step-2".
>
> However, I found this step is offseted by 0.5 * dt.
> Then the timing is different of dumping coordinates and velocities.
>
> So, I want to get force information at the same timing
> when coorinates and velocities are written down.
Amber uses a leap-frog algorithm, so velocities and coordinates are always out
of step by dt/2. The forces are determined from the coordinates, so those two
are in sync with each other.
If you look at where the total energy is computed, you can see that the
velocities are interally computed "on step" as well (in order to compute the
kinetic energy that is printed out). Hence it should be possible to get the
coordinates, velocities and forces all at a single time point, but you'll have
to grok the code to figure out exactly how to do that.
..good luck...dac
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Received on Sat Apr 27 2013 - 04:30:02 PDT
