[gmx-users] genconf and bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 26 16:19:28 CEST 2011

Fabio Affinito wrote:
> Hi all,
> I used genconf because I wanted to replicate a membrane with ion channel 
> on the xy plane:
> genconf -f conf.gro -o out.gro -nbox 2 2 1
> Then I edited by hand the .top file where I modified the number of 
> molecules in the system.
> When attempting to run, disregarding the number of processors, the mdrun 
> crashes because domain decomposition fails.
> Looking with attention to the log I find this:
>> 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: 30.871 nm, LJ-14, atoms 193657 193660
>>     multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659
>>     Minimum cell size due to bonded interactions: 33.959 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: 0.44
>>     Will use 2304 particle-particle and 1792 PME only nodes
>>     This is a guess, check the performance at the end of the log file
>>     Using 1792 separate PME nodes
>>     Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>     Optimizing the DD grid for 2304 cells with a minimum initial size 
>> of 42.448 nm
>>     The maximum allowed number of cells is: X 1 Y 1 Z 0
> Now, I'm wondering why do I have such big bond interation length.. 31nm!
> I guess that the problems in the DD arises from this.
> Can you give me some suggestions?

Were the molecules whole in the coordinate file you replicated?  If not, the 
bonds will now be assigned across the entire box.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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