[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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