[gmx-users] Contradiction beetwen Domain Decomposition in PME and the use of SPECBOND

[Justin Lemkul]

On 7/1/16 8:50 AM, Олег Шавыкин wrote:
>  Dear All,
>
> We tried to make simulation of lysine dendrimer (with repeat unit consisting of one branched lysine (LYH) and two linear lysine (CLYO and LYS) in each generation) using SPECBOND command to create branched structure.
> We use next specbond.dat file:
>
> 1
> CLYO    C       1       LYH     NZ      1       0.151   CLYO    LYH
>
> We use PME for calculation of electrostatics interactions which use Domain Decomposition program.
> Simulation is running well on single processor on PC using command:
>
> mdrun -s trp_md.tpr -o trp_md.trr -c trp_pmd.gro -g md.log -e md.edr
>
> or on 4 processors on PC using command:
>
> mpirun -n 4 mdrun -dlb no -s trp_md.tpr -o trp_md.trr -c trp_pmd.gro -g md.log -e md.edr
>
> We use here option "-dlb no", because mpirun for our task doesn't work on PC without it and give error message similar to that
> on big computer (see below).
>
> However, it doesn't work on supercomputer using command:
>
> sbatch -n 64 -J task -t 5 -p test ompi /home/users/user1/_scratch/gromacs/bin/mdrun -dlb no -s trp_md.tpr -o traj.xtc -c trp_end.gro -npme 32 -v
>
> We use same approach and the same command on supercomputer for similar molucule before (without SPECBOND) and it works O'K.
>
> In the case of SPECBOND we have got next error message:
>
> Initializing Domain Decomposition on 64 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.410 nm, LJ-14, atoms 830 838
>   multi-body bonded interactions: 4.442 nm, Improper Dih., atoms 496 495

Bonded interactions should not occur over such distances; inspect the topology 
to make sure it is actually sound.  These atoms will tell you what's going on.

-Justin

> Minimum cell size due to bonded interactions: 4.886 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.763 nm
> Estimated maximum distance required for P-LINCS: 0.763 nm
> Using 32 separate PME nodes, per user request
> Optimizing the DD grid for 32 cells with a minimum initial size of 4.886 nm
> The maximum allowed number of cells is: X 2 Y 2 Z 2
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.6
> Source code file: domdec.c, line: 6436
>
> Fatal error:
> There is no domain decomposition for 32 nodes that is compatible with the given box and a minimum cell size of 4.88592 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> We tried change number of nodes and used mdrun option -rdd, but without success.
>
> We use next md.mdp:
>
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  50000000 ; total 100 ns.
> nstcomm             =  1
> nstxtcout           =  1000
> nstxout             =  0
> nstvout             =  0
> nstfout             =  0
> nstlog              =  50000
> nstenergy           =  5000
> nstlist             =  10
> ns_type             =  grid
> coulombtype = PME
> rvdw = 0.9
> rlist = 0.9
> rcoulomb = 0.9
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  v-rescale
> tc-grps             =  Protein     SOL   CL
> tau_t               =  0.1     0.1   0.0
> ref_t               =  300     300   300
> ; Energy monitoring
> energygrps          =  Protein     SOL    CL
> ; Isotropic pressure coupling is now on
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  371925
>
> please, help us
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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