[gmx-users] Structure optimization failure

[Lara Bunte]

Hello

I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure minimization. I made a file pr.mdp. Could you please tell me, what I could do better in this file, or what is wrong? I guess there has to be something wrong, because GROMACS failed with grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr with the error: "Water molecule starting at atom 3924 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
"


My pr.mdp file is:


title           = lumiflavin NPT equilibration
define      = -DPOSRES  ; position restrain the protein

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000         ; 2 * 50000 = 100 ps
dt              = 0.002         ; 2 fs

; Output control
nstxout         = 5000          ; save coordinates every 4 ps
nstvout         = 5000          ; save velocities every 4 ps
nstenergy       = 5000          ; save energies every 4 ps
nstlog          = 5000          ; update log file every 4 ps


; Bond parameters
continuation    = yes           ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic 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         = 10             ; edited to 1
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT

; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Isoalloxazin Sol   ; two coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl          = berendsen     ; Pressure coupling on in 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 = all

; Velocity generation
gen_vel     = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed


Thank you for helping me
Greetings
Lara