[gmx-users] DNA-Protein complex MD failing

[virginia miguel]

Hi everyone; I am tryingto run a simulation of a DNA-protein complex obtained by docking of a dsDNA of18bp to a crystal structure of the recA protein using GPU. I used amber ff, adodecahedron cell with 15A of distance from the surface of the complex and neutralizedwith counter ions (42 NA+, since my system charge is -42). I minimized with steepest descendent for 4000 steps and the obtainedenergies are ok, this is my minimization mdp

define      = -DFLEXIBLE
constraints = none
integrator  = steep
dt          = 0.001 ; ps !
nsteps      = 10000
nstlist     = 10
ns_type     = grid
rlist       = 1.0
coulombtype = PME
rcoulomb    = 1.0
vdwtype     = cut-off
rvdw        = 1.0
fourierspacing = 0.08
fourier_nx     = 0
fourier_ny     = 0
fourier_nz     = 0
pme_order      = 8
ewald_rtol     = 1e-5
optimize_fft   = yes
;
; Energy minimizing stuff
;
emtol          = 1000.0
emstep         = 0.01

 But when Iintend to run de md protocol a segmentation error occurs and the dynamicsbreaks. I have tried to start with NVT and NPT ensembles, with positionrestrictions of all, the backbone and no restrictions at all. Also with temperaturesas low as 100K but it the dynamics keep on blowing up. I have these warnings 

"Step 663, time 0.663 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 329.431423, max 141697.812500 (between atoms 17283 and 17284)
bonds that rotated more than 30 degrees"
---and finally--
"
WARNING: Listed nonbonded interaction between particles 12971 and 12990
at distance 2.320 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


./rungromacs: line 10:  8006 Segmentation fault "


I do notknow what the correct settings of .mpd …I am using the following that resultsfroma a review I did of several works working with DNA and amber in gromacs. This is my md .mdp
 title = AMBER
define = -DFLEXIBLE
cpp = /usr/bin/cpp -traditional

; RUN CONTROL PARAMETERS
                  integrator = md
; Start time and timestep in ps
                       tinit = 0
                          dt = 0.002
                     nsteps  = 100000

; mode for center of mass motion removal
                  comm-mode  = Linear
; number of steps for center of mass motion removal
                    nstcomm  = 1
; group(s) for center of mass motion removal
                  comm_grps  = system


; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000

; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000

; Output frequency for energies to log file and energy file
nstlog                   = 5000
nstenergy                = 5000

; Output frequency and precision for xtc file
nstxtcout                = 5000
xtc-precision            = 1000

; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc_grps                 = !SOL

; Selection of energy groups
energygrps               = !SOL SOL

; NEIGHBOR SEARCHING
                 nstlist = 10
                 ns_type = grid
                     pbc = xyz
; nblist cut-off
                   rlist  = 1.2

; domain-decomposition    = no


; ELECTROSTATICS
                  rcoulomb = 1.0
               coulombtype = PME
; EWALD
fourierspacing             = 0.10
pme_order                  = 6
ewald_rtol                 = 1e-5
optimize_fft               = yes


; VDW
vdwtype                    = switch 
rvdw_switch                = 0.8  
rvdw                       = 1.0    




; TEMPERATURE COUPLING
Tcoupl                    = berendsen
tau_t                     = 0.1 0.1 0.1
tc-grps                   = SOL  DNA  Protein
ref_t                     = 100  100  100

; PRESSURE COUPLING
Pcoupl                    = no


; VELOCITY GENERATION
gen_vel                   = yes
gen_temp                  = 100
gen_seed                  = 173529

; BONDS
constraints               = all-bonds
constraint_algorithm      = LINCS


Issomeone can give me a hint of where I am failing I would appreciate it indeed.Sincerely, Virginia. 
 Dra. Virginia Miguel
Instituto de Investigaciones Biológicasy Tecnológicas (IIBYT)
CONICET-UNC
I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)