[gmx-users] pulling simulation

[Mehrnoosh Hazrati]

Dear all,

I'm trying to do umbrella sampling. But after running "perl distances.pl",
I get a "summary_distances.dat file which has NO distances! Before, I get
an error "pull reference distance for group 1 is negative" while I run
grompp and then mdrun for pulling simulation.

Below is my pull_md.mdp file.

Thank you for any help and suggestion.

Regards
Mehrnoosh

P.S.
I'm using gromacs v4.5.7


pull_md.mdp file:

title       = Umbrella pulling simulation
; Run parameters
integrator  = md
dt          = 0.001
tinit       = 0
nsteps      = 5000000    ; 5 ns
nstcomm     = 10
; Output parameters
nstxout     = 1000      ; every 10 ps
nstvout     = 1000
nstfout     = 500
nstxtcout   = 500       ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 10
ns_type     = grid
rlist       = 1
rcoulomb    = 1
rvdw        = 1
; 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      = V-rescale
tc_grps     = DPPC  DRG  SOL
tau_t       = 0.5   0.5  0.5
ref_t       = 310   310  310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = semiisotropic
tau_p           = 2.0   2
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   = distance
pull_dim        = N N Y
pull_start      = yes
pull_ngroups    = 1
pull_group0     = LIPID
pull_group1     = DRUG
pull_init1      =  0
pull_rate1      = -0.01
pull_k1         = 500     ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps