[gmx-users] Using TIP4P(2005) with GROMOS-53a6

[Pallavi Banerjee]

Hello users,

I am simulating a polymer in TIP4P(2005) water with GROMOS53a6 as the force
field. I am using the same mdp options as has been provided in the source
website. The following error shows up:

" Molecule type 'SOL' has 6 constraints.
  For stability and efficiency there should not be more constraints than
  internal number of degrees of freedom: 3 "

I tried a sample run with just the water, but the same happens. Could
someone provide some valuable insight?

Following are the mdp options:

; RUN CONTROL
integrator               = md
nsteps                   = 500000
dt                       = 0.001
; NEIGHBOR SEARCHING
cutoff-scheme            = Verlet
nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.85
domain-decomposition     = no
; OUTPUT CONTROL
nstxout                  = 10000
nstvout                  = 10000
nstxtcout                =10000
nstlog                   =1000
nstenergy                =1000
; OPTIONS FOR BONDS     =
constraints              = all-angles
; Type of constraint algorithm =
constraint-algorithm     = shake
; Do not constrain the start configuration =
unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 1e-6
; Highest order in the expansion of the constraint coupling matrix =
lincs-order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no

; OPTION FOR ELECTROSTATIC AND VDW
coulombtype              = PME
rcoulomb_switch          = 0
rcoulomb                 = 0.85
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon_rf                = 3.5
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw_switch              = 0
rvdw                     = 0.85
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1.0
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used
;fourier_nx               = 0
;fourier_ny               = 0
;fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
;epsilon_surface          = 0
;optimize_fft             = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl                   =  V-rescale
tc_grps                  =  System
tau_t                    =  10
ref_t                    =  300
Pcoupl                   = no
;Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 10
compressibility          = 5.0e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300


Thanks and regards,
Pallavi Banerjee.