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

[Yulian Gavrilov]

No, at this point I am not applying any special conditions.

On 28 September 2017 at 03:23, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
Sincerely,
Yulian Gavrilov