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

[Justin Lemkul]

On 2/5/14, 11:05 AM, Steven Neumann wrote:
> Maybe you know how do they keep nanotubes rigid then?
>

Nope, sorry.

-Justin

>
> On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann <s.neumann08 at gmail.com
> <mailto: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
>     <mailto: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
>         <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>         <tel:%28410%29%20706-7441>
>         http://mackerell.umaryland.__edu/~jalemkul
>         <http://mackerell.umaryland.edu/~jalemkul>
>
>         ==============================__====================
>         --
>         Gromacs Users mailing list
>
>         * Please search the archive at
>         http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List
>         <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before
>         posting!
>
>         * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>         <http://www.gromacs.org/Support/Mailing_Lists>
>
>         * For (un)subscribe requests visit
>         https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-users
>         <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or
>         send a mail to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>
>
>

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

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

==================================================