[gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition

[Justin Lemkul]

On 9/25/17 6:57 AM, Yulian Gavrilov wrote:
> Dear all,
> 
> I try to restrain the conformation of a protein using distance/bonds
> restrains.
> I have a problem when I try to use distance restraints or restraint
> potential (bonds type 10) together with domain decomposition.
> 
> I use gromacs2016.3. It seems that this issue should be solved for 2016
> version:
> http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html
> [Made distance restraints work with threads and DD]
> 
> However, I get an error (both for bonds and distance restraints):
> 
> Fatal error:
> There is no domain decomposition for 8 ranks that is compatible with the
> given
> box and a minimum cell size of 9.15291 nm
> Change the number of ranks or mdrun option -rdd or -dds [this does not help]
> Look in the log file for details on the domain decomposition
> 
> 
> 
> My steps:
> 
> 1. Add to .top file:
> 
> [ bonds ]
> ; ai   aj   type    low     up1     up2     kdr
>    43   87     10    0.28     0.31    0.33     1000
>    53  107     10    0.28     0.31    0.33     1000
> ...
> 
> or
> 
> [ distance_restraints ]
> ; ai   aj   type   index   type'      low     up1     up2     fac
>    43   87      1       0       1      0.28    0.31    0.33    1.0
>    53  107      1       0       1      0.28    0.31    0.33    1.0
> ...
> 
> in case of  [ distance_restraints ] I add to mdp file:
> disre           = simple; simple or ensemble
> ;nstdisreout=0
> disre-fc        = 1000; [kJ mol^-1 nm^-2]
> 
> 2. Run it with this script:
> 
> #PBS -q sleep -l select=8:ncpus=8:mem=5000mb
> ...
> echo Using modules `module list`
> setenv OMP_NUM_THREADS 8
> ...
> module load mkl/11.3.4.258  gcc/4.9.3  impi/5.1.3.258
> source /usr/local/gromacs-2016.3/bin/GMXRC.csh
> ...
> mpirun gmx_mpi mdrun -v -deffnm md100ns
> 
> 
> Please can you suggest something or explain what I am doing wrong?
> 

A minimum DD cell size of 9 nm seems unrelated to distance restraints of 0.3 nm. 
Are you applying any other strange conditions? Free energy code or custom 
exclusions?

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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