[gmx-users] Domain decomposition configuration
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 10 02:45:09 CET 2011
Mark Abraham wrote:
> On 10/02/2011 8:10 AM, Justin A. Lemkul wrote:
>>
>>
>> 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.
>
> And you will then have potential issues with clashing atoms, so need to
> re-equilibrate. Unfortunately, in general there is no box definition
> where all molecules are whole and inside the box, and it's certainly not
> worthwhile looking for one.
>
Not worthwhile? In the case of the OP's problem, there's no way out unless you
make the molecules whole. You certainly can't have it both ways (both whole and
in the box, but take, for instance, atoms A and B in the same molecule, which
are bonded. The normal situation across PBC:
| |
-B A-
| |
is fine. DD can re-establish the proper bond across PBC. But if this system is
concatenated to one with water (*):
| |******|
-B A--------
| |******|
the bond is physically unrealistic and DD fails. Even if you *could* get the
simulation to run (i.e. in serial or mdrun -pd), it would instantly crash due
either to LINCS failure or some such problem. So making the molecules whole
prior to concatenation gives:
| |******|
| A-B*****|
| |******|
which works. Of course, you do have to worry about clashes, so maybe
concatenation is not the best approach, but rather a run through genbox would be
more suitable.
-Justin
> Mark
>
>>
>> -Justin
>>
>>> On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>> 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
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>
>>> <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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