[gmx-developers] accessing atoms position with domain decomposition

[Massimiliano Bonomi]

Dear Gromacs Developers,

I would like to make the external plugin PLUMED working with
gromacs 4 and the domain decomposition.
This plugin adds additional forces on selected atoms.
For this reason, the plugin needs to access to the position of these  
atoms
at every time step.

Is there an efficient way to accomplish this when using domain  
decomposition?

Since this is a problem related to many computational technique, such as
steering, umbrella sampling..., have you planned to develop a general  
interface
which makes the position of a list of atoms available at request  
without compromising
the parallel efficiency of the code?

Best regards,
Massimiliano

--------------------------------------------------------------------------------------------------------
ETH Zürich
Massimiliano Bonomi
Computational Science, Department of Chemistry and Applied Biosciences,
c/o USI Campus, via Giuseppe Buffi 13,
CH-6900 Lugano, Switzerland

mbonomi at ethz.ch
massimiliano.bonomi at gmail.com

http://www.rgp.ethz.ch

+41 58 666 48 03           phone
+41 58 666 48 17           fax
massimiliano.bonomi    skype