[gmx-users] Domain decomposition configuration
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 10 03:18:57 CET 2011
Mark Abraham wrote:
> On 10/02/2011 12:45 PM, Justin A. Lemkul wrote:
>>
>>
>> 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.
>
> Sure, whole molecules are necessary for the OP's approach, but my point
> is that it is not worthwhile looking for a box with all of the molecules
> whole *and* inside the (pre-concatenation) box (e.g. by trying new box
> centers), because in general there need not be one.
>
Ah, now I understand what you were saying. Good point, and certainly more
generally true than the specific case I was thinking of.
-Justin
> Mark
>
>> 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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