[gmx-users] Martini+elastic network

Enrico Spiga spiga.enrico at gmail.com
Wed May 6 18:13:34 CEST 2009

Dear all,
I am trying to run an energy minimization of a protein using Martini model +
Elastic Network.
I created correctly the itp file adding the constrain for the elastic

when I try to submit the job on 32 processors I get the following:

<Initializing Domain Decomposition on 32 nodes
<Dynamic load balancing: no
<Will sort the charge groups at every domain (re)decomposition
I<nitial maximum inter charge-group distances:
<    two-body bonded interactions: 0.593 nm
<  <multi-body bonded interactions: 1.133 nm
<Minimum cell size due to bonded interactions: 1.246 nm
<Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 3.434 nm
<Estimated maximum distance required for P-LINCS: 3.434 nm
<This distance will limit the DD cell size, you can override this with -rcon
<Optimizing the DD grid for 32 cells with a minimum initial size of 3.434 nm
<The maximum allowed number of cells is: X 3 Y 3 Z 2
<Program mdrun_d, VERSION 4.0
<Source code file: domdec.c, line: 5651

<Fatal error:
<There is no domain decomposition for 32 nodes that is compatible with the
given box and a minimum cell size of 3.4336 nm
<Change the number of nodes or mdrun option -rcon or your LINCS settings
<Look in the log file for details on the domain decomposition

and clearly the job stops.

What I should do?

Thank you very much in advance


Reality is that wich, when you stop believing in it, doesn't go away.
Philip K. Dick

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090506/b0105a65/attachment.html>

More information about the gromacs.org_gmx-users mailing list