[gmx-users] Re: umbrella sampling

[Thomas Schlesier]

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-request at 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