[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

[Steven Neumann]

Dear Gmx Users,

I am running REMD of a small protein in water. I have 36 temperatures.
After minimization I equilibrate each with nvt and npt ensemble. Then I
start REMD with -multidir. The mdp:


; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000000
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0       ; save coordinates every 0.2 ps
nstvout     = 0       ; save velocities every 0.2 ps
nstenergy   = 5000       ; save energies every 0.2 ps
nstxtcout   = 5000
nstlog      = 5000
; Bond parameters
continuation    = no           ; first dynamics run
constraint_algorithm = lincs    ; holoyesmic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5         ; 10 fs
vdwtype     = Switch
rvdw-switch = 1.0
rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = Protein Water_and_ions   ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 320.12   320.12                     ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
gen_temp    = 320.12
DispCorr    = EnerPres  ; account for cut-off vdW scheme
gen_seed   = 173529
gen_vel     = yes       ; assign velocities from Maxwell distribution


I get the error: step 12005: Water molecule starting at atom 7030 can not
be settled. I tried to repeat it and I get the same error with another
water molecule at different step. I am using Gmx 4.5.5

I tried minimization many times lowering the maximum force by steepest
descent, make the time step 1fs in equilibtration but it does not help. I
changed to force field as well and the same is happening. Please, advise.

Steven