[gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition
Yulian Gavrilov
yulian.gavrilov at gmail.com
Fri Sep 29 22:18:06 CEST 2017
Dear Justin,
Thank you for making me check the log file attentively. I completely forgot
that there was an additional restrain of a dihedral angle.
This angle is problematic and bonds restraint is fine, When I run without
this dihedral restrain DD works fine. No problem, my bad.
However, now I have a question:
In addition to bond restraints I need to introduce a dihedral restraint
that 'connects' atoms in two different domains (in order to prevent domain
rotations).
How can I do it with DD? The dihedral restraint 'connects' atoms on a big
distance (see the log).
>From the log:
Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.581 nm, Restraint Pot., atoms 65 131
multi-body bonded interactions: 6.657 nm, Dih. Rest., atoms 1471 2902
Minimum cell size due to bonded interactions: 7.322 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
Estimated maximum distance required for P-LINCS: 0.819 nm
Using 0 separate PME ranks, as there are too few total
ranks for efficient splitting
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 9.153 nm
The maximum allowed number of cells is: X 1 Y 1 Z 1
On 28 September 2017 at 14:52, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>
>>> ==================================================
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>>> Gromacs Users mailing list
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>>>
>>
>>
> --
> ==================================================
>
> 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
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--
Sincerely,
Yulian Gavrilov
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