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

[Florian Altvater]

Hi,
I don't know if my question somehow got lost, or if I forgot to provide
some necessary information. Anyway it would be of great help to me, if
someone could tell me her/his opinion on the problem. I need to use
particle decomposition as I want to introduce distance restraints from
2-6nm, which domain decomposition can't handle apparently.

Thanks again for your help
Florian

Am 19.09.2011 14:30, schrieb Florian Altvater:
> 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.
> Regards,
> Florian
>


-- 
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