Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules
whole again?
The only way, as far as I'm aware (aside from editconf's crude approach). Do
this before you concatenate your systems.
-Justin
On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>> 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>
<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> <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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