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

[Mark Abraham]

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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>