[gmx-users] genconf and bonded interactions

[Fabio Affinito]

On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
>
>
> Fabio Affinito wrote:
>> This is the mdrun output:
>>
>> Initializing Domain Decomposition on 4096 nodes
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>> two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705
>> multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704
>> Minimum cell size due to bonded interactions: 33.035 nm
>> Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
>> 1.139 nm
>> Estimated maximum distance required for P-LINCS: 1.139 nm
>> Guess for relative PME load: 0.43
>> Will use 2400 particle-particle and 1696 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> Using 1696 separate PME nodes
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 2400 cells with a minimum initial size of
>> 41.293 nm
>> The maximum allowed number of cells is: X 0 Y 0 Z 0
>>
>> -------------------------------------------------------
>> Program mdrun_mpi_bg, VERSION 4.5.4
>> Source code file: domdec.c, line: 6438
>>
>> Fatal error:
>> There is no domain decomposition for 2400 nodes that is compatible
>> with the given box and a minimum cell size of 41.2932 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>> Look in the log file for details on the domain decomposition
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>
> This is bizarre. Did you fix the periodicity of the original coordinate
> file (conf_start.gro) and rebuild the system, or did you try to run
> trjconv on the replicated system? The former is the correct approach.
>
> -Justin
>
This is what I did (in the chronological order):

1) trjconv -f conf_start.gro -o conf_whole.gro -pbc whole
2) genconf -f conf_whole.gro -o out.gro -nbox 2 2 1
3) i modified the topol.top (modifying the number of molecules)
4) grompp -f grompp.mdp -c out.gro -p topol.top  -maxwarn 3
5) launched mdrun

Fabio
-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198