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

[Steven Neumann]

Maybe you know how do they keep nanotubes rigid then?


On Wed, Feb 5, 2014 at 3:58 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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>
>