[gmx-users] Umbrella pulling Drug + Ion channel

[Andres Ortega]

Dear gromacs users, i ´ve beem trying to get the geometries of a drug
molecule permeating an ion channel,
the drug molecule is in a greater Z position than the Protein, but i always
get the error :"Segmentation fault (core dumped)"
this is my .mdp

title       = Umbrella pulling simulation DOX
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 250000    ; 500 ps
nstcomm     = 10
; Output parameters
nstxout     = 5000      ; every 10 ps
nstvout     = 5000
nstfout     = 500
nstxtcout   = 500       ; every 1 ps
nstenergy   = 500

cutoff-scheme = Verlet

; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes             ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 20
ns_type     = grid
rlist       = 1.2
rcoulomb    = 1.2
rvdw        = 1.2
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     = Protein  POPC Water_and_ions_DOX
tau_t       = 1.0    1.0   1.0
ref_t       = 310    310   310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = semiisotropic
tau_p           = 1.0      
compressibility = 4.5e-5 4.5e-5
ref_p           = 1.0   1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull            = umbrella
pull_geometry   = cylinder  ;
pull_vec1       = 0.0 0.0 1.0 ;
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = DOX
pull-r1 = 1.0
pull-r0 = 1.0
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 800      ; kJ mol^-1 nm^-2
pull_pbcatom0   = 8485

According with other post, i have to select a pull_pbcatom0 closes to the
middle of my reference ( an atom close to the middle of the ion channel's
pore) and a pull_vec1 positive even if the drug is "above" the channel, i
was wondering if you could help me with this, or giving me an advice of this
error, thanks in advance

Andrés Ortega

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