[gmx-users] umbrella sampling

[Nawel Mele]

HI,

I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the  constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:

title       = Umbrella pulling simulation
; 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
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; 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     = domain_1 domain_2
tau_t       = 0.5    0.5
ref_t       = 310    310*
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 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            = constraint
pull_geometry   = distance  ; simple distance increase
pull_dim        = Y Y Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 2
pull_group0     = domain_1
pull_group1     = domain_2
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2*


I don't know if I use the good option for compute this king of umbrella
sampling.
When I run the grompp command: *grompp -f md_pull.mdp -c min1.gro -p
topol.top -n index.ndx -o pull.tpr* I optain this error:
*
Fatal error:
108147 atoms are not part of any of the T-Coupling groups*


I am little confuse with the mdp file option. I don't know which name I
should clarify for  "T-Coupling groups" ( in green) ??

If some one can help me .
THanks a lot.

Nawel


-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg