[gmx-users] accleration group

[Erik Lindahl]

Rui Qiao wrote:

> Dear All:
>         In using Gromacs to do NEMD, I apply an accleration to each atom
> in the system and when I run "grompp", it shows me a message like:
>
>         "Net Acceleration in X direction, will be corrected"
>
>         What does this means?
>
>         Thanks for your time.
>
>         sincerely,
>
>         Rui
> ------------------------
> Rui Qiao
> Research Assistant
> Beckman Institute, UIUC

Well, if you move the entire system the only effect will be a motion
relative to
the completely arbitrary location of the periodic boundary conditions. All
interactions between the particles will be identical to a non-moving system
- ideally.

The reason we correct this type of accelerations is they build up a
velocity
(a.k.a. "flying ice cube in free space") that will lead to numerical errors

in single precision. (when we try to add the very small interparticle force
to the
huge force on the system).

Normally when you pull stuff you want use some kind of reaction force
group, e.g.
pull an ion while the reaction force is applied to the ionchannel and
membrane.

But of course we can change it if you have some good idea why it should be
possible
to pull the entire systems :-)

Cheers,

Erik