<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.</div><div> I am doing Umbrella sampling using plumed-gromacs. for that i have done umbrella pulling using gromacs only <br></div><div>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)</div><div>when i do the sampling using
plumed-gromacs i used gromacs mdp files with option of tinit =120 while i define all these extracted pdbs (from 120 to 360ns) in plumed .dat file . is it appropriate ? i Think when plumed-gromacs do the sampling, it consider from 120 to 360 ns trajectories only. is it correct?. i have provided the plumed.dat and md.mdp file as below kindly consider and go through it . i am expecting your valuable reply</div><div> 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</div><div><br></div><div><br></div><div>title = Umbrella pulling 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<br><br></div></div></body></html>