Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are two updates for velocities and then the update for
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are
Yes, I understand that. But my question is more about why the two velocity
updates are implemented before the position update and not the other way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t +
Because the 'start' of the vv integrator step is halfway through the loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the same
loop and 2) minimizing communication and output. It is not as elegant as
it should be. There are efforts to clean this up, but it's a lot of
Thank you very much Professor Shirts.
I have these doubts because I am trying to implement new integrators based
in the concatenation of two VV steps to make a single step. The idea
follows the integrators suggested in
http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
This is
Yes, I've been using the theory here:
http://arxiv.org/abs/1301.3800
Which describes how to concantenate integrator steps in a formal way.
I can say that the time savings you get by concatenating integrators is
VERY small. The only time it is nonnegligible is when there is a LOT of
Thank you very much for this reference. I will take a look at it carefully.
We are trying to develop and implement this integrators for hybrid Monte
Carlo simulations and our interest is not really related to time saving but
to sampling efficiency.
Right now it doesn't look straightforward to me
Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns
out to be non-trivial for the bookkeeping. The easiest way to do this
was split the velocity Verlet updates.
Also, the additional computational cost of two half steps for
velocities is trivial compared to the cost of the
