[gmx-users] Domain decomposition configuration
Denny Frost
dsfrost at cableone.net
Wed Feb 9 22:09:16 CET 2011
Is tpbconv with the "pbc" option the best way to make the molecules whole
again?
On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul <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>> 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>>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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