Dear jusitn Thank you for your previous reply. I am doing Umbrella sampling using plumed-gromacs. for that i have done umbrella pulling using gromacs only I have extracted the frame of reference from 120ps to 360ps . i am using these set of trajectories for the Umbrella sampling in plumed gromacs (interface with plumed) when i do the sampling using plumed-gromacs i used gromacs mdp files while i define all these extracted pdbs (from 120 to 360ns) in plumed .dat file .My question is whould could restraint ? is it possoible to set restraint as Zero in umbrella sampling . in plumed interface gromacs restraints is set after key word AT .Here i am setting zero . is it appropriate? Because in one gromacs mailing list said that there is no need to set position restraint for umbrella sampling so i have set 0 after key word AT so please go through the following link I am expecting your valuable reply http://lists.gromacs.org/pipermail/gmx-users/2011-June/062433.html PRINT W_STRIDE 100 S_PATH TYPE RMSD FRAMESET mdoutput NFRAMES 24 LAMBDA 72.634290 Z_PATH TYPE RMSD FRAMESET mdoutput NFRAMES 24 LAMBDA 72.634290 UMBRELLA CV 1 KAPPA 1000 AT 0.000000 UMBRELLA CV 2 KAPPA 1000 AT 0.000000 ENDMETA
title = Umbrella sampling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 120 nsteps = 250000 ; nstcomm = 10 ; Output parameters nstxout = 50 ; nstvout = 50 nstfout = 50 nstxtcout = 50 nstenergy = 50 ; 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 = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) ;annealing = periodic single ; Number of time points to use for specifying annealing in each group ;annealing_npoints = 5 3 ; List of times at the annealing points for each group ;annealing_time = 0 3 6 9 12 0 2 4 ; Temp. at each annealing point, for each group. ;annealing_temp = 310 320 298 298 310 310 320 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; 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 ; simple distance increase ;pull_dim = N N Y ;pull_start = yes ; define initial COM distance > 0 ;pull_ngroups = 1 ;pull_group0 = Chain_B ;pull_group1 = Chain_A ;pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns ;pull_k1 = 1000 ; kJ mol^-1 nm^-2
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