[gmx-developers] Reference coordinates in mdrun - Availability at all nodes

[Mark Abraham]

Tsjerk Wassenaar wrote:
> Hi,
> 
> For some reason, I'm reading in a set of reference coordinates in
> mdrun (do_md). These should be available during the entire run, but
> obviously, I have to ensure that they are available at each node in
> order not to compromise efficiency. Could any of you give a pointer
> (no pun intended, but please, not a void pointer :p) on how to achieve
> that?

It won't be straightforward. The DD algorithm doesn't replicate full 
position arrays across processors, so there's a bunch of messy indexing 
that goes on. Presumably you'll need to subject your reference 
coordinates to the same decomposition so that indices match on the 
nodes. If so, you can just add another rvec * to t_forcerec, load it 
earlier, and use the global vs local machinery that's already used for 
the positions. I suggest stepping through the (start of the) DD in the 
do_md loop.

Mark