>Stanislav Bobritsky wrote: >>* Hello dear gromacs users! *>*> I`m trying to do targeted MD. I have two protein conformations which are
*>*> different from each other by one loop position. I need to force *>*> conformation A to B. *>*> It was following commands executed: *>*> *>*> grompp -с box.gro -f md.mdp -r conf1.pdb -rb conf2.pdb -p topol.top -o *>*> transformer.tpr *>*> *>* > mdrun -s transformer.tpr -o -x -c -e -g -v *>*> *>*> But it can be viewed from traj.xtc that conformation didn`t change. *>*> Protein just spins (with speed increasing), and desired loop does not move. *>*> *>* > What can I do to fix it? *> >What's in your .mdp file? > >Mark .mdp file contains following: title = prot cpp = cpp define = -DFLEX_SPC integrator = md tinit = 0 dt = 0.001 nsteps = 1000000 init_step = 0 comm-mode = Linear nstcomm = 1 comm-grps = bd-fric = 0 ld-seed = 1993 emtol = 1000.0 emstep = 0.001 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 nstxout = 1000 nstvout = 2000 nstfout = 2000 nstcheckpoint = 10000 nstlog = 100 nstenergy = 1000 nstxtcout = 1000 xtc-precision = 1000 xtc-grps = protein ;SOL UNK CL- energygrps = protein ;SOL UNK CL- nstlist = 10 ns_type = Grid pbc = xyz rlist = 0.9 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r = 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1 energygrp_table = fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No tcoupl = berendsen tc-grps = protein ; sol CL- UNK tau_t = 0.1 ; 0.1 0.1 0.1 ref_t = 298 ; 298 298 298 Pcoupl = no Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 1.0 1.0 andersen_seed = 815131 gen-vel = no gen-temp = 298 gen-seed = 173529 constraints = all-bonds constraint-algorithm = Shake unconstrained-start = yes Shake-SOR = no shake-tol = 1e-04 lincs-order = 4 lincs-iter = 2 lincs-warnangle = 60 morse = no energygrp_excl = 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 dihre-tau = 0 nstdihreout = 100 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 Stanislav Bobritsky, ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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