[gmx-users] handling particle decomposition with distance restraints
jayant james
jayant.james at gmail.com
Thu Jun 25 03:01:26 CEST 2009
I just replaced the old gmx 4.0 version with the 4.0.5 version and still the
same problem
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
On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> jayant james wrote:
>
>> 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!!
>>
>
> Upgrade to the latest version (4.0.5), since there have been numerous
> improvements to domain decomposition throughout the development of version
> 4.0.
>
> -Justin
>
> 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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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp)
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