Hey ! My doubt posted few days back still holds. I am trying to simulate the kinase domain in complex with cyclin. when i keep entire complex either position restrained or flexible, MD runs without any errors. But as soon as i keep cyclin position restrained keeping kinase domain flexible, it gives errors.
Initially it gave LINCS warnings saying fatal error that charged group at atom xxxxxx moved more than distance allowed by DD in direction X. Error persists even if i repeat the same procedure this time equilibrating the system for 150ps instead of usual 40ps. the pdb file obtained after equilibration appears perfect without any breaks. As suggested by Justin, I also tried to check if my system is blowing up. But when i take co-ordinates of last frame, i get few random fragments having no 3D structure/ interconnections. Here is .top file that i am using: title = KD with Cyc PR test run ;warnings = 10 cpp = /usr/bin/cpp define = -DPOSRES_B ; with DPOSRES it works fine. without any define option also it works fine constraints = all-bonds integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 comm_mode = Linear nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid pbc = xyz rlist = 2.0 coulombtype = PME rcoulomb = 2.0; in nm units vdwtype = cut-off rvdw = 2.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temp coupling: on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling: on Pcoupl = parrinello-rahman tau_p= 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities gen_vel = yes gen_temp = 300.0 gen_seed = 173529 I wish to do MD with increased electrostatic and VdW cut-offs. Chain B is Cyclin and A is kinase domain.
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