Re: [gmx-users] Domain decomposition configuration

[Mark Abraham]

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 <jalem...@vt.edu 
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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

                  ========================================
                  --     gmx-users mailing list    gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@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 or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.

                  Can't post? Read
        http://www.gromacs.org/Support/Mailing_Lists



           --     ========================================

           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

           ========================================
           --     gmx-users mailing list    gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@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 or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
           Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



    --     ========================================

    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

    ========================================
    --     gmx-users mailing list    gmx-users@gromacs.org
<mailto:gmx-users@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 or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




--
gmx-users mailing list    gmx-users@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 or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists