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
--
========================================
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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