[gmx-users] Long range restraints problem

Gregor Hagelueken hagelueken at pc.uni-bonn.de
Fri Oct 19 11:32:07 CEST 2018


I am trying to simulate a protein complex with Gromacs. I have followed this tutorial http://cgmartini.nl/~mdcourse/md.html <http://cgmartini.nl/~mdcourse/md.html> and everything works fine.

However, my aim is to add long range distance restraints from PELDOR/DEER spectroscopy to the simulation (6-8 nm long). My approach was to do this as described here:
http://cgmartini.nl/~mdcourse/pepmd/resmd.html <http://cgmartini.nl/~mdcourse/pepmd/resmd.html>

So, I included the distance information like so:
[ bonds ]
; atom i j  func low up1 up2 fc
247     4014 10   7.5 7.5 8.5 120.0 

When I start the simulation, I get this error:
There is no domain decomposition for 64 ranks that is compatible with the given box and a minimum cell size of 8.5455 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

Does this mean that the start and end point of the “bond” have to be in the same box/cell? It would be really large then…

Is there any way around this? Do I need to approach this completely differently?

Thanks for your help!


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