[gmx-users] particle decomp crashes while domain decomp das not

Florian Altvater Florian.Altvater at physchem.uni-freiburg.de
Mon Sep 19 14:30:33 CEST 2011

Hi there,
I haven't found a post describing this problem, so here I am.

I'm running GROMACS 4.3.5 with the OPLS-AA force-field and the TIP3P
water model on a 170kDa protein dimer with sodium ions to neutralize the
charges. I added two new residues to the force-field (which seem to
behave normally). Now the problem:

When I run with domain decomposition everything works fine during 9ns.
The structure seems to equilibrate more or less and the overall domain
conformation doesn't seem to alter much.

When I switch on particle decomposition, however, the simulation crashes
after 2-3ns due to a lincs warning. It seems to happen always at the
same residue, Arg318 which gets pulled/pushed out of the helix it is in.
The closest modified residue is 326 which doesn't seem to be disturb the
system too much.

Anyway it seems strange to me that the method of decomposition seems to
change the outcome of the simulation a lot (and does not only reflect in
the computing time). Now I don't understand too much of the algorithms
used. And as I couldn't find anything bout adjusting parameters if using
the one or the other I'm a bit in the dark about what to do now.

Did you have similar experiences? How do you suggest that I tackle the
problem? Do you need more information? In case it is of any relevance
here the parameters of the mdp file:

    dt                       = 0.002
    nsteps                   = 1500000
    comm-grps                = system
    nstxout                  = 20000
    nstvout                  = 20000
    nstfout                  = 20000
    nstlog                   = 20000
    nstcalcenergy            = 1
    nstxtcout                = 500
    xtc-grps                 = protein
    energygrps               = protein
    ns_type                  = grid
    rlist                    = 1.0
    coulombtype              = PME
    vdw-type                  = Cut-off
    rcoulomb                 = 1.0
    rvdw                     = 1.0
    DispCorr                 = EnerPres
    tcoupl                   = V-rescale
    tc-grps                  = Protein Non-Protein
    tau_t                    = 0.1    0.1
    ref_t                    = 325     325
    pcoupl                   = Parrinello-Rahman
    pcoupltype               = isotropic
    tau_p                    = 2.0
    compressibility          = 4.5e-5
    ref_p                    = 1.0
    andersen_seed            = -1
    gen_vel                  = no
    gen-temp                 = 325
    gen-seed                 = -1
    constraints              = all-bonds
    constraint_algorithm     = lincs
    continuation             = yes
    lincs_order              = 4
    lincs_iter               = 1
    disre                    = simple
    disre_weighting          = conservative
    disre_fc                 = 800
    disre_tau                = 0

Thank you very much.

Florian Altvater
Albert-Ludwigs-Universität Freiburg
Institut für Physikalische Chemie - Lehrstuhl I
Albertstr. 21
79104 Freiburg, Germany

Phone: +49 (761) 203-6210
Fax: +49 (761) 203-6222
E-Mail: Florian.Altvater at physchem.uni-freiburg.de

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