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? Thank you very much in advance -- Enrico Reality is that wich, when you stop believing in it, doesn't go away. Philip K. Dick --
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
