[gmx-users] membrane region fixed

[Patricia Saenz Méndez]

Hi!
I am trying to run a simulation of a membrane protein (without the
membrane), and to this end I am trying to fix the region of the protein
that is inserted in the hydrophobic part of the membrane. It is not a
transmembrane protein, just an helix is"touching" the lipophylic part of
the membrane.
I used genrestr and an index file. I could equilibrate the system. But when
trying to run the actual MD simulation (200 ns) I just get the calculation
finished in a couple of minutes and apparently just run 100 ps (like during
equilibration).
There it goes the command line (gromacs 5.1):

mpirun -np 200 gmx_mpi grompp -f md_NPT_200ns.mdp -c 1w6j-wild_npt.gro -t
1w6j-wild_npt.cpt -p 1w6j-wild.top -n index.ndx -o 1w6j-wild_md_200ns.tpr

mpirun -np 200 gmx_mpi mdrun -s 1w6j-wild_npt.tpr -deffnm 1w6j-wild_md_200ns

and the mdp file:

define      = -DPOSRES_MEMBRANE ; position restrain the membrane region
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 100000000  ; 2 * 100000000 = 200000 ps (200 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout             = 5000000         ; save coordinates every 100.0 ps
nstvout             = 5000000         ; save coordinates every 100.0 ps
nstenergy           = 2500            ; save energies every 5.0 ps
nstlog              = 25000          ; update log file every 50.0 ps
nstxtcout           = 2500           ; write .xtc trajectory every 5.0 ps
energygrps          = Protein
; Bond parameters
continuation    = yes           ; 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
cutoff-scheme   = Verlet
ns_type         = grid      ; search neighboring grid cells
nstlist         = 5         ; 10 fs, largely irrelevant with Verlet
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  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein    ; 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
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
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution


What am I doing wrong?
Thanks in advance,

P