Dear all, <div><br></div><div>I am trying to run an energy minimization of a protein using Martini model + Elastic Network.</div><div>I created correctly the itp file adding the constrain for the elastic network.</div><div>
<br></div><div>when I try to submit the job on 32 processors I get the following:</div><div><br></div><div><br></div><div><div><Initializing Domain Decomposition on 32 nodes</div><div><Dynamic load balancing: no</div>
<div><Will sort the charge groups at every domain (re)decomposition</div><div>I<nitial maximum inter charge-group distances:</div><div>< two-body bonded interactions: 0.593 nm</div><div>< <multi-body bonded interactions: 1.133 nm</div>
<div><Minimum cell size due to bonded interactions: 1.246 nm</div><div><Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 3.434 nm</div><div><Estimated maximum distance required for P-LINCS: 3.434 nm</div>
<div><This distance will limit the DD cell size, you can override this with -rcon</div><div><Optimizing the DD grid for 32 cells with a minimum initial size of 3.434 nm</div><div><The maximum allowed number of cells is: X 3 Y 3 Z 2</div>
<div><</div><div><-------------------------------------------------------</div><div><Program mdrun_d, VERSION 4.0</div><div><Source code file: domdec.c, line: 5651</div><div><br></div><div><Fatal error:</div>
<div><There is no domain decomposition for 32 nodes that is compatible with the given box and a minimum cell size of 3.4336 nm</div><div><Change the number of nodes or mdrun option -rcon or your LINCS settings</div>
<div><Look in the log file for details on the domain decomposition</div><div>-<------------------------------------------------------</div><div><br></div><div>and clearly the job stops.</div><div><br></div><div>What I should do?</div>
<div><br></div><div>Thank you very much in advance</div><div><br></div><br>-- <br>Enrico<br><br>Reality is that wich, when you stop believing in it, doesn't go away.<br>Philip K. Dick<br><br>--<br>
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