[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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