[gmx-users] Problems with distance restraints

[Justin A. Lemkul]

Please disregard my message.  I had a typo in my atom numbers that I was 
restraining.  Apparently the distance between atoms 1016 and 559 is far greater 
than 0.376 nm, thus generating the error.

-Justin

Justin A. Lemkul wrote:
> 
> Hi all,
> 
> I am trying to use a simple scheme to restrain a few distances within my 
> protein, which is contained within an octahedral box of SPC water.
> 
> In place of distance restraints, I'm using bond type 6 to utilize a 
> harmonic potential to restrain the distance between a few atoms.  When I 
> imposed one such restraint in the topology, the simulation ran fine.  
> After finishing this trajectory, I wanted to impose a second restraint 
> and try again.  At this point, the simulation fails with the following:
> 
> mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt
> 
> <snip>
> 
> Initializing Domain Decomposition on 24 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: 1.634 nm
>   multi-body bonded interactions: 0.606 nm
> Minimum cell size due to bonded interactions: 1.797 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
> Estimated maximum distance required for P-LINCS: 0.876 nm
> Guess for relative PME load: 0.45
> Will use 12 particle-particle and 12 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 12 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm
> The maximum allowed number of cells is: X 2 Y 2 Z 2
> 
> -------------------------------------------------------
> Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2
> Source code file: domdec.c, line: 5842
> 
> Fatal error:
> There is no domain decomposition for 12 nodes that is compatible with 
> the given box and a minimum cell size of 2.24633 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------
> 
> "I'm Only Faking When I Get It Right" (Soundgarden)
> 
> I realize there are more optimizations I could impose to better balance 
> the PP/PME load.  I have tried those (altering my cutoff's and grid 
> spacing) but it makes no difference.  Plus, I'd like to remain 
> consistent with the original simulation that used only one restraint.  
> If I remove the second restraint, the simulation runs just fine.  For 
> reference, the restraints I'm imposing are:
> 
>   330  1016     6    0.669   5.0300e+06
>  1016   559     6    0.376   5.0300e+06
> 
> The box vectors from the .gro file are:
> 
>    7.14132   6.73290   5.83086   0.00000   0.00000   2.38044   0.00000 
> -2.38044   3.36645
> 
> Is there anything obvious that I'm doing wrong?  Or should I just use 
> real distance restraints, according to manual section 4.3.4?  Thanks for 
> any insights.
> 
> -Justin
> 

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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