[gmx-users] Problems in mdrun - CHARMM27

[Lara Bunte]

Hello

Could you please take a look on my new pr.mdp file that I created for equilibrating water around lumiflavin. grompp works but I guess there must be something wrong because after grompp I am using mdrun and get this warning:

Warning: 1-4 interaction between 1 and 5 at distance 2.429 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


step 1: Water molecule starting at atom 8655 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates


My system is lumiflavin in a dodecahedron box, a tip3p water model and the CHARMM27 force field. This is my pr.mdp file:

title           = Lumiflavin NVT equilibration 
define          = -DPOSRES    
; Run parameters
integrator      = md           
nsteps          = 50000        ; 2 * 50000 = 100 ps
dt              = 0.002            ; 2 fs
; Output control
nstxout         = 100           ; save coordinates every 0.2 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100          ; save energies every 0.2 ps
nstlog          = 100            ; update log file every 0.2 ps
; Bond parameters
continuation    = no            ; first dynamics run
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         = 5                ; 10 fs
rlist           = 1.2               ; short-range neighborlist cutoff (in nm)
rlistlong       = 1.4
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 is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = ISO 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 off
pcoupl          = no            ; no pressure coupling in NVT
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed

Thanks for helping me

Best greetings
Lara