[gmx-users] Martini+elastic network

[Justin A. Lemkul]

Enrico Spiga wrote:
> 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 
> network.
> 
> 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?

First, upgrade to the most current version (4.0.4) - it contains many 
improvements and bugfixes.

Second, take the advice mdrun is giving you.  Your system cannot be split into 
32 pieces.  Either change the desired number of processors, or modify the 
options mdrun has indicated.  More information is availabe in the manual, the 
Gromacs 4 paper, and in the list archive, as this problem has been raised before.

-Justin

> 
> Thank you very much in advance
> 
> 
> -- 
> Enrico
> 
> Reality is that wich, when you stop believing in it, doesn't go away.
> Philip K. Dick
> 
> --
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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