Dear sir: Thank you for reading my letter. I have a few problems in Shell MD
.... . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help. And this is my own *.mdp file below include = define = integrator = sd tinit = 0 dt = 0.004 nsteps = 10000000 simulation_part = 1 init_step = 0 comm-mode nstcomm = Linear = 100 comm-grps = System bd-fric = 1 ld-seed = 1993 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 1000000 nstvout = 1000000 nstfout = 1000000 nstlog = 10 nstenergy = 10 nstxtcout = 10 xtc_precision = 10 xtc-grps = energygrps = CR1 nstlist = 1 ns_type = grid pbc = xyz periodic_molecules = no rlist = 2.0 coulombtype = User rcoulomb_switch = 0.0 rcoulomb = 2.0 epsilon_r = 1 epsilon_rf = 1 vdw_type = User rvdw_switch = 0.0 rvdw = 2.0 DispCorr = No table_extension = 0 energygrp_table = CR1 CR1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes implicit_solvent = No gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_epsilon_solvent = 80 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 tcoupl = berendsen tc-grps = System tau_t = 0.3 ref_t = 800 Pcoupl = no Pcoupltype = isotropic tau_p = 1 compressibility = 6.5e-5 ref_p = 5.0 refcoord_scaling = No andersen_seed = 815131 QMMM = no QMMM-grps = QMmethod = QMMMscheme = normal QMbasis = QMcharge = QMmult = SH = CASorbitals = CASelectrons = SAon = SAoff = SAsteps = MMChargeScaleFactor = 1 bOPT = bTS = annealing = annealing_npoints = annealing_time = annealing_temp = gen_vel = yes gen_temp = 313 gen-seed = 173529 constraints = none constraint_algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 1e-04 lincs_order = 4 lincs-iter = 1 lincs_warnangle = 30 morse = no energygrp_excl = nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 pull = no disre = No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 100 orire = no orire-fc = 0 orire-tau = 0 orire-fitgrp = nstorireout = 100 dihre = no dihre-fc = 1000 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = E-x = E-xt = E-y = E-yt = E-z = E-zt = user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 Could you tell me which part of the parameter should be changed for Shell MD? Your prompt attention to this letter would be highly appreciated. Thanks a lot. Liyan
-- 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