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

[Justin Lemkul]

On 9/28/17 2:11 AM, Yulian Gavrilov wrote:
> No, at this point I am not applying any special conditions.

The full section of the .log file pertaining to DD setup would be useful 
here. We're just seeing the last bit, but how mdrun constructs the DD 
cells based on topological information often provides clues.

-Justin

> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>

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

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

==================================================