[gmx-users] No domain decomposition

[Mark Abraham]

Hi,

If your topologies are all good, then you will be able to run each kind of
molecule in this system in a box on its own. Your symptoms suggest that you
will not be able to do this :-) If you try it, then you will either prove
they're good, or find at least one bad one.

Mark

On Thu, Sep 24, 2015 at 5:30 PM soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Hi Justin and Tsjerk,
>                                   thanks for your valuable suggestions.
> Justin, I am attaching the structure of my system after the energy
> minimization step i.e, as follows
>
>
> https://drive.google.com/file/d/0B7SBnQ5YXQSLbEdhZEZKVUtJTHM/view?usp=sharing
>
> I dont see any distortion in the structure. But when I proceed for position
> restrained dynamics, I am getting the following error on issuing mdrun
> -deffnm nvt
>
> Step 910:
> The charge group starting at atom 1539 moved more than the distance allowed
> by the domain decomposition (3.333333) in direction Z
> distance out of cell -8.503349
> Old coordinates:    4.604    5.037    4.690
> New coordinates:   -3.702    5.989   -5.170
> Old cell boundaries in direction Z:    3.333    6.667
> New cell boundaries in direction Z:    3.333    6.667
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.6
> Source code file: domdec.c, line: 4124
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
>
>
> Then following Tsjerk's advice, I issued mdrun -deffnm nvt -nt 8 after
> which I get the same error. I can't understand what's going wrong from the
> .log file.
>
> There are: 98940 Atoms
> Charge group distribution at step 0: 4039 4205 4385 4423 4386 4270 4317
> 4241
> Grid: 5 x 15 x 15 cells
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 0.00e+00
> Initial temperature: 397.477 K
>
> Started mdrun on node 0 Thu Sep 24 08:52:44 2015
>
>            Step           Time         Lambda
>               0        0.00000        0.00000
>
>    Energies (kJ/mol)
>           Angle            U-B    Proper Dih.  Improper Dih.          LJ-14
>     2.97004e+03    3.84714e+02    1.17214e+04    3.55064e+02    3.34059e+04
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>    -1.60787e+03    2.88658e+05   -1.89372e+03   -2.01160e+06   -3.71978e+04
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     9.46864e+00   -1.71480e+06    2.87409e+05   -1.42739e+06   -1.42739e+06
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.50934e+02   -6.28921e+01   -4.78393e+05    2.81540e-02
>
> DD  step 4 load imb.: force  5.6%
>
> DD  step 499 load imb.: force  6.0%
>
>            Step           Time         Lambda
>             500        0.50000        0.00000
>
>    Energies (kJ/mol)
>           Angle            U-B    Proper Dih.  Improper Dih.          LJ-14
>     2.15265e+04    4.81825e+03    2.24841e+04    5.26390e+02    7.79415e+04
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>    -1.90445e+03    3.20893e+05   -1.89372e+03   -1.94686e+06   -3.66598e+04
>  Position Rest.      Potential    Kinetic En.   Total Energy  Conserved En.
>     2.39384e+04   -1.51519e+06    2.47287e+05   -1.26790e+06   -1.13929e+06
>     Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     3.01944e+02   -6.28921e+01   -1.66734e+02    4.42351e-04
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.6
> Source code file: domdec.c, line: 4124
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Chemical gases filling lungs of little ones" (Black Eyed Peas)
>
> If anybody knows how to settle this issue I will really appreciate it. As
> of now I can't see a way out apart from setting up the system again. But I
> am 100% sure that there was nothing wrong with the topologies.
>
> Thanks and regards,
> Soumadwip Ghosh
> Research Fellow
> IITB
> Mumbai
> India
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