Hi,
it seems that you've only coupled your protein to the thermostat, but
not the solvent, hence the error message.
Generally one would couple both domains of the protein to one thermostat
and the solvent (inluding ions) to another thermostat.
Side note: If you want to use the WHAM method for constructing the PMF
from the simulations, you need to use an harmonic potential instead of
constraints. This method is named 'umbrella sampling'.
Using constraints and integrating the constraint force to obtain the PMF
is called 'thermodynamic integration'.
Greetings
Thomas
Am 13.05.2013 10:33, schrieb gmx-users-requ...@gromacs.org:
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
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