Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error:
Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 50000 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 4.4832208e+19 Maximum force = inf on atom 14524 Norm of force = inf gcq#182: "That Was Cool" (Beavis and Butthead) -----My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 50000 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy = 500 nstxtcout = 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist = 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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
