[gmx-users] There is no domain decomposition for nodes that is compatible

[Steven Neumann]

Thanks. May I also ask why when changing bonds (with lincs = none ) into
constraints (lincs) I have huge deviations and the simulation crahes?
Is it possible to apply bonds or constraints between two molecules type?

Steven


On Wed, Feb 5, 2014 at 4:14 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Depends on the size of your system and how much parallelism you want to
> use. See manual section on DD.
>
> Mark
>
>
> On Wed, Feb 5, 2014 at 4:58 PM, Steven Neumann <s.neumann08 at gmail.com
> >wrote:
>
> > Thank you. Can you specify what does long mean? Is there any limit?
> >
> >
> > On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 2/5/14, 10:46 AM, Steven Neumann wrote:
> > >
> > >> Can you please advise? With large constraints it does not work...
> with [
> > >> distance_restraints ] it works but only with mdrun -nt 1
> > >> my mdp:
> > >>
> > >> disre                =  simple
> > >> disre-fc             =  1000
> > >>
> > >> integrator               = md
> > >> tinit                    = 0.0
> > >> dt                       = 0.008
> > >> nsteps                   = 100000      ; 500 ns
> > >> nstcomm                  = 100
> > >> nstcalcenergy         = 100
> > >>
> > >> nstxout             = 0
> > >> nstvout               = 0
> > >> nstenergy            = 0
> > >> nstlog                   = 100
> > >> nstxtcout                = 100
> > >>
> > >> freezegrps         = System
> > >> freezedim          = N N Y
> > >> energygrps               = ACI BAS GLY NON POL
> > >> energygrp_table          = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS
> > BAS
> > >> BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL
> POL
> > >> table-extension         = 1.0
> > >>
> > >>
> > >> nstlist                  = 10
> > >> ns_type                  = grid
> > >> pbc                      = xyz
> > >> rlist                    = 2.0
> > >>
> > >>
> > >> coulombtype          = User
> > >> rcoulomb                 = 2.0
> > >>
> > >> vdw_type                 = User
> > >> rvdw                     = 2.0
> > >>
> > >>
> > >> tcoupl               = V-rescale
> > >> tc_grps               = System
> > >> tau_t                 = 0.1
> > >> ref_t                 = 300
> > >> pcoupl             = no
> > >>
> > >> gen_vel                  = yes
> > >> gen_temp                 = 300
> > >> gen_seed                 = -1
> > >>
> > >>
> > >> constraints              = none
> > >> constraint_algorithm     = Lincs
> > >> continuation             = no
> > >> lincs_iter              = 1
> > >> lincs_order              = 4
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> I will really appreciate.
> > >>
> > >>
> > > DD cells are set up based on bonded geometry and a host of other
> factors.
> > >  Any very long bond or restraint will seriously inhibit the ability of
> DD
> > > to function.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > 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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