Hi Justin, Here is my complete code for umbrella sampling
title = Umbrella pulling simulation define = -DPOSRES_2 integrator = md dt = 0.002 tinit = 0 nsteps = 2500000 ; 5 ns nstcomm = 10 nstxout = 50000 ; every 100 ps nstvout = 50000 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 constraint_algorithm = lincs constraints = all-bonds continuation = yes 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 = V-rescale tc_grps = Protein SOL tau_t = 0.5 0.5 ref_t = 300 300 ; 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 pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 I will do this umbrella sampling for 10ns, Do you think the COM distance can converge after long simulation time? ie back to the restraint position. Regards, Vijay. > Vijayaraj wrote: > > Hello, > > > > I am doing umbrella sampling to calculate PMF curve for the detachment > > of a terminal cyclic peptide with 8 aa's (CP) from the self-assembled > > cyclic peptide nanotube. I extracted the reaction coordinates staring > > from 5.5 ang COM distance between the terminal CP and the 2nd CP to 17.5 > > ang, I did umbrella sampling on 25 configurations (for 5ns) and the > > window size is 0.5 ang. I used the following pulling code for umbrella > > sampling, > > > > pull = umbrella > > pull_geometry = distance > > pull_dim = N N Y > > pull_start = yes > > pull_ngroups = 1 > > pull_group0 = Chain_B > > pull_group1 = Chain_A > > pull_init1 = 0 > > pull_rate1 = 0.0 > > pull_k1 = 1000 > > pull_nstxout = 1000 > > pull_nstfout = 1000 > > > > > > I restrained the 2nd CP unit and the pull_rate1 is 0, so the COM > > distance between the chain_A (terminal) and chain_B (2nd CP) should be > > restrained. after 5ns of umbrella sampling, I calculated the COM > > distance between chain A and B, but it was not restrained, for the 5.5 > > ang COM distance restrain, the COM distance varies from 4.5 to 5.5 ang. > > and also the pulling cyclic peptide undergoes large conformational > > sampling. from the WHAM analysis I understood the sampling window is > > poorly represented. In addition to COM distance restrain, can I restrain > > the pulling CP's backbone atoms? so that the pulling groups large > > conformational sampling will be reduced. > > You could implement dihedral restraints to fix the backbone secondary > structure, > but I can't comment on the stability of trying to use these restraints in > addition to the pull code. Seems like a lot going on at once, to me. > > Also consider the fact that 5 ns is an extremely short timeframe to gather > meaningful data. Perhaps you just need more time in each window to > equilibrate. > At the shortest COM distance, your two molecules are still likely > experiencing > some interactions, and it may require a great deal of sampling in this > window to > converge the simulations. You haven't shown the rest of your .mdp file > (always > a good idea!), so we can only guess at whether or not your other settings > should > lead to a sensible result. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
