<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear jusitn Thank you for your previous reply.<br> I am doing Umbrella sampling using plumed-gromacs. for that i have done umbrella pulling using gromacs only<br>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)<br>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 <span style="font-weight: bold;">to set position restraint</span> for umbrella <br> sampling so i have set 0 after key word AT so please go through the <br> following link I am expecting your valuable reply<br> <a target="_blank" rel="nofollow" href="http://www.google.com/url?sa=D&q=http://lists.gromacs.org/pipermail/gmx-users/2011-June/062433.html&usg=AFQjCNEtYxJVjDi3YS6B0OkXEIrSfqoKlw">http://lists.gromacs.org/pipermail/gmx-users/2011-June/062433.html</a> <br> PRINT W_STRIDE
100<br> S_PATH TYPE RMSD FRAMESET mdoutput NFRAMES 24 LAMBDA 72.634290<br> Z_PATH TYPE RMSD FRAMESET mdoutput NFRAMES 24 LAMBDA 72.634290<br> UMBRELLA CV 1 KAPPA 1000 AT 0.000000<br> UMBRELLA CV 2 KAPPA 1000 AT 0.000000<br> ENDMETA<br><br><br>title = Umbrella sampling simulation<br>define = -DPOSRES_B<br>; Run parameters<br>integrator = md<br>dt = 0.002<br>tinit = 120<br>nsteps = 250000 ;<br>nstcomm = 10<br>; Output
parameters<br>nstxout = 50 ;<br>nstvout = 50<br>nstfout = 50<br>nstxtcout = 50 <br>nstenergy = 50<br>; Bond parameters<br>constraint_algorithm = lincs<br>constraints = all-bonds<br>continuation = yes ; continuing from NPT<br>; Single-range cutoff scheme<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.4<br>rcoulomb = 1.4<br>rvdw = 1.4<br>; PME electrostatics parameters<br>coulombtype = PME <br>fourierspacing =
0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = Nose-Hoover<br>tc_grps = Protein Non-Protein<br>tau_t = 0.5 0.5<br>ref_t = 310 310<br>; SIMULATED ANNEALING <br>; Type of annealing for each temperature group (no/single/periodic)<br>;annealing = periodic single<br>; Number of time points to use for specifying annealing in each
group<br>;annealing_npoints = 5 3<br>; List of times at the annealing points for each group<br>;annealing_time = 0 3 6 9 12 0 2 4<br>; Temp. at each annealing point, for each group.<br>;annealing_temp = 310 320 298 298 310 310 320 310<br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 1.0 <br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocities is off<br>gen_vel = no<br>; Periodic boundary conditions are on in all directions<br>pbc = xyz<br>; Long-range
dispersion correction<br>DispCorr = EnerPres<br>; Pull code<br>;pull = umbrella<br>;pull_geometry = distance ; simple distance increase<br>;pull_dim = N N Y<br>;pull_start = yes ; define initial COM distance > 0<br>;pull_ngroups = 1<br>;pull_group0 = Chain_B<br>;pull_group1 = Chain_A<br>;pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns<br>;pull_k1 = 1000 ; kJ mol^-1 nm^-2</div></div></body></html>