[gmx-users] SHAKE error

[Justin Lemkul]

On 7/22/16 7:59 AM, gozde ergin wrote:
> No I am using same Gromacs 4.6.5.
> I run these two simulations again one runs and the other fails with the same .mdp file.
>

Since the error is DD-specific, probably your earlier run did not include the 
same exact setup, either in terms of number of processors or in terms of the 
topology (note specific reference to constraints crossing charge group boundaries).

-Justin

>> On 22 Jul 2016, at 13:53, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 7/22/16 7:50 AM, gozde ergin wrote:
>>> Dear all,
>>>
>>> I use md-vv and SHAKE algorithm however I face an error which I was not before.
>>> Before I had 1-decanol and water system and now I have cis-pionic and water system.
>>>
>>> I exactly use the same .mdp file just as before however this error comes :
>>> SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS
>>>
>>> Do you have any idea why I am getting this error which I was not getting before?
>>>
>>
>> Probably you were using a different version of the code before.  Various feature combinations get disabled as suitable tests are not run or bugs are found. LINCS is more stable, anyway, so just use it instead and the run should work.
>>
>> -Justin
>>
>>> MDP FILE:
>>>
>>>
>>> integrator               = md-vv
>>> dt                       = 0.002
>>> nsteps                   = 8000000   ; 16 ns
>>> ; Output control
>>> nstxout                  = 2000
>>> nstvout                  = 2000
>>> nstlog                   = 2000
>>> nstenergy                = 2000
>>> ; Bond parameters
>>> continuation         = no        ; Initial simulation
>>> constraint_algorithm = shake     ; holonomic constraints
>>> constraints          = all-bonds ; all bonds (even heavy atom-H bonds) constrained
>>> shake_tol            = 0.0001
>>> ; Neighborsearching
>>> ns_type     = grid              ; search neighboring grid cels
>>> nstlist     = 5                 ; 10 fs
>>> rlist       = 1.2               ; short-range neighborlist cutoff (in nm)
>>> rcoulomb    = 1.2               ; short-range electrostatic cutoff (in nm)
>>> rvdw        = 1.2               ; short-range van der Waals cutoff (in nm)
>>> ; Electrostatics
>>> coulombtype     = PME           ; Particle Mesh Ewald for long-range electrostatics
>>> pme_order       = 4             ; cubic interpolation
>>> fourierspacing  = 0.16          ; grid spacing for FFT
>>> ; Temperature coupling
>>> ; tcoupl is implicitly handled by the sd integrator
>>> tcoupl                   = nose-hoover
>>> tc-grps                  = System
>>> tau_t                    = 1.0
>>> ref_t                    = 300
>>> ; Periodic boundary conditions
>>> pbc     = xyz                   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr    = EnerPres          ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel     = yes               ; Velocity generation is on
>>> gen_temp    = 300               ; temperature for velocity generation
>>> gen_seed    = -1                ; random seed
>>> ; COM motion removal
>>> ; These options remove COM motion of the system
>>> nstcomm         = 10
>>> comm-mode       = Linear
>>> comm-grps       = System
>>>
>>>
>>>
>>> thanks
>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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