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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists