Denny Frost wrote:
This run is actually a combination of two 5x5x5 nm boxes, one if which
was previously run in DD, and the other is water. Since the length of
that bond is almost 5 nm, is it possible that the pbc's are not being
recognized? There is no way I have a bond that long from my previous run.
I'll venture a guess that there were broken molecules in the system you
concatenated? That would gel with a bond that stretches across a 5-nm box. You
have to deal with whole molecules in the input configuration.
-Justin
On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Denny Frost wrote:
I'm using version 4.5.3
Here's the output from the log file from DD initiation to the error:
Initializing Domain Decomposition on 8 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: 4.893 nm, Bond, atoms 8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
Minimum cell size due to bonded interactions: 5.382 nm
Bonded interactions should normally not occur over such a length.
The information printed here points to the culprits. What are
these atoms, and why are they bonded if they are so far away?
-Justin
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size
of 6.728 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.5.3
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 8 nodes that is compatible
with the given box and a minimum cell size of 6.72787 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
And here is my mdp file
title = BMIM+PF6
cpp = /lib/cpp
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 75000 ; total 150 ps
nstcomm = 10
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = Cut-off
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = BMI PF6 SOL tau_t
= 0.2 0.2 0.2
ref_t = 300 300 300
nsttcouple = 1
; Energy monitoring
energygrps = BMI PF6 SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = BMI PFF
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Denny Frost wrote:
I am trying to start a run using domain decomposition on a
5x5x10 nm box with about 26,000 atoms in it. I've tried
running
8-16 pp nodes, but gromacs always throws an error saying that
there is no domain decomposition compatible with this box
and a
minimum cell size of 6.728 nm. I've tried many values
for -dds
and a few dd vectors, but with no luck. Does anyone know
to get
domain decomposition working on a rectangular system like
this?
Not without significantly more information. Please post:
1. Your Gromacs version
2. Any DD-related information that is printed to either the
log file
or stdout
3. Your .mdp file
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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