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 <jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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