Dear All<br><br>I have a file which contains afew residues (noncontinuous),<br>When I use mdrun on a computer(4 cpu) I am facing with the following Error:<br><br>Fatal error:<br>There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 3.28697 nm<br>
Change the number of nodes or mdrun option -rdd<br>Look in the log file for details on the domain decomposition<br><br><br>it is relating to domain decomposition,<br>Besides I checked either restraining residues and not restraining.But it dosn't differed<br>
<br>I changed the number of nodes to 1 but it didn't work!<br>mpirun -np 1 mdrun -v -deffnm EM <br><br>Besides I looked in the log file and the important part of it was:<br><br>Initializing Domain Decomposition on 4 nodes<br>
Dynamic load balancing: no<br>Will sort the charge groups at every domain (re)decomposition<br>Initial maximum inter charge-group distances:<br> two-body bonded interactions: 2.988 nm, LJ-14, atoms 922 943<br> multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943<br>
Minimum cell size due to bonded interactions: 3.287 nm<br>Using 0 separate PME nodes<br>Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm<br>The maximum allowed number of cells is: X 1 Y 1 Z 1<br>
<br><br>please let me know how can I solve this problem.<br>Thanks in advance<br>