[gmx-users] accleration group
lindahl at stanford.edu
Tue Jan 22 04:50:52 CET 2002
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.
> Rui Qiao
> Research Assistant
> Beckman Institute, UIUC
Well, if you move the entire system the only effect will be a motion
the completely arbitrary location of the periodic boundary conditions. All
interactions between the particles will be identical to a non-moving system
The reason we correct this type of accelerations is they build up a
(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
huge force on the system).
Normally when you pull stuff you want use some kind of reaction force
pull an ion while the reaction force is applied to the ionchannel and
But of course we can change it if you have some good idea why it should be
to pull the entire systems :-)
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