Fabio Affinito wrote:
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
Presumably in conjunction with a .tpr file, in order for this to work?
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
What are the warnings you are trying to circumvent? Please provide the full
grompp output. I can think of a few other possibilities for the source of your
problem, but I do not want to venture idle guesswork without seeing all of the
warnings you've got.
-Justin
5) launched mdrun
Fabio
--
========================================
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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