[gmx-users] Domain decomposition configuration

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 10 03:16:38 CET 2011


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.

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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>>>
>>
>




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