[gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition
jalemkul at vt.edu
Thu Sep 28 13:52:42 CEST 2017
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.
> 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
>>> 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
>>> [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
>>> box and a minimum cell size of 9.15291 nm
>>> Change the number of ranks or mdrun option -rdd or -dds [this does not
>>> 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
>>> [ 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
>>> 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/188.8.131.528 gcc/4.9.3 impi/184.108.40.2068
>>> 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 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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