[gmx-users] SHAKE error

gozde ergin gozdeeergin at gmail.com
Fri Jul 22 13:50:10 CEST 2016


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?

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


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