[gmx-users] Domain decomposition configuration
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Feb 10 01:31:59 CET 2011
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.
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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