<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><meta http-equiv="x-dns-prefetch-control" content="off"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Hey !<br><br>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. <br><br>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.<br><br>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.<br><br>Here is .top file that i am
using:<br><br>title = KD with Cyc PR test run<br>;warnings = 10<br>cpp = /usr/bin/cpp<br>define = -DPOSRES_B ; with DPOSRES it works fine. without any define option also it works fine<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002<br>nsteps = 5000<br>nstcomm = 1<br>comm_mode = Linear<br>nstxout = 10<br>nstvout = 10<br>nstfout = 10<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 2.0<br>coulombtype = PME<br>rcoulomb = 2.0; in nm units<br>vdwtype = cut-off<br>rvdw = 2.0<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 temp coupling: on<br>Tcoupl = v-rescale<br>tau_t = 0.1 0.1<br>tc-grps = protein non-protein<br>ref_t = 300 300<br>; Pressure coupling: on<br>Pcoupl = parrinello-rahman<br>tau_p= 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocities<br>gen_vel = yes<br>gen_temp =
300.0<br>gen_seed = 173529<br><br></div>
<br>I wish to do MD with increased electrostatic and VdW cut-offs. Chain B is Cyclin and A is kinase domain.<br></div><meta http-equiv="x-dns-prefetch-control" content="on">
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