[gmx-users] handling particle decomposition with distance restraints
jayant james
jayant.james at gmail.com
Thu Jun 25 01:58:06 CEST 2009
Hi!
I am performing an mpi MD (on a quad core system) run with distance
restraints. When I execute this command below without position restraints
the MD run is distributed over 4 nodes perfectly well. But when I
incorporate the distance restraints I hit a road block
mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro &
I get this error message (below). My pr.mdp and distance restraints files
are given below the error message
. *
Question.* How do I handle this sitation? Do I increase the long range cut
off in the pr.mdp file? If you see my distance restraints file, my upper
range of distances are close to 9nm!!
Please guide.
Thanks
JJ
----------------------------------------------------------------------------------------------------------------------------------------------------------
Back Off! I just backed up md.log to ./#md.log.6#
Reading file pr.tpr, VERSION 4.0 (single precision)
NOTE: atoms involved in distance restraints should be within the longest
cut-off distance, if this is not the case mdrun generates a fatal error, in
that case use particle decomposition (mdrun option
-pd)
WARNING: Can not write distance restraint data to energy file with domain
decomposition
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.2
Source code file: domdec.c, line: 5842
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 9.85926 nm
Change the number of nodes or mdrun option -rdd or
-dds
Look in the log file for details on the domain
decomposition
-----------------------------------------------------------------------------------------------------------------------------------------------
*pr.mdp*
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
cpp = /usr/bin/cpp
define = -DDISRES
constraints = none
;constraint_algorithm = lincs
;lincs_order = 4
integrator = md
dt = 0.001 ; ps !
nsteps = 4000000 ; total 2.0ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstlog = 50000
nstenergy = 500
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
disre = simple
disre_weighting = equal
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein Non-Protein
;tnc Non-Protein tnt NMR tni
; Pressure coupling is not on
Pcoupl = parrinello-rahman
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
;simulated annealing
;Type of annealing form each temperature group (no/single/periodic)
;annealing = no, no, no, single, no
;
;Number of annealing points to use for specifying annealing in each group
;annealing_npoints = 0, 0, 0, 9, 0
;
; List of times at the annealing points for each group
;annealing_time = 0 25 50 75 100 125 150 175 200
; Temp.at each annealing point, for each group.
;annealing_temp = 300 350 400 450 500 450 400 350 300
*
distance restraints file*
distance_restraints ]
; ai aj type index type' low up1 up2 fac
;TnT240-TnI131, 145, 151, 160, 167 (ca+-7)
2019 3889 1 1 1 3.91 3.91 5.31
0.574679
2019 4056 1 2 1 4.86 4.86 6.26
0.409911
2019 4133 1 3 1 5.69 5.69 7.09
0.457947
2019 4207 1 4 1 6.63 6.63 8.03
0.323852
2019 4273 1 5 1 7.14 7.14 8.54
0.294559
;TnT276- Tni 131,145,151,160,167,5,17,27,40
2434 3889 1 6 1 1.34 1.34 2.74
4.884769
2434 4056 1 7 1 2.13 2.13 3.53
0.523368
2434 4133 1 8 1 3.66 3.66 5.06
0.409911
2434 4207 1 9 1 4.48 4.48 5.88
0.547825
2434 4273 1 10 1 5.43 5.43 6.83
0.285938
2434 2628 1 11 1 5.89 5.89 7.29
0.241333
2434 2719 1 12 1 4.76 4.76 6.16
0.366358
2434 2824 1 13 1 3.81 3.81 5.21
0.644145
2434 2972 1 14 1 3.10 3.10 4.50
0.431009
;TnT288- Tni 131,145,151,160,167,5,17,27,40
2557 3889 1 15 1 1.89 1.89 3.29
1.429688
2557 4056 1 16 1 3.25 3.25 4.65
0.32931
2557 4133 1 17 1 4.44 4.44 5.84
0.346847
2557 4207 1 18 1 4.80 4.80 6.20
0.275198
2557 4273 1 19 1 5.84 5.84 7.24
0.200744
2557 2628 1 20 1 4.79 4.79 6.19
1.046736
2557 2719 1 21 1 5.06 5.06 6.46
0.267659
; 2557 2824 1 22 1
2557 2972 1 23 1 3.99 3.99 5.39
0.412797
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