I also checked the output of the minimization: Steepest Descents converged to machine precision in 402 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.81875038188621e+04 Maximum force = 3.20769543152855e+02 on atom 331 Norm of force = 2.04356801849931e+01
I assume the structure is not relaxed enough to start a simulation. How can I get it minimize further? I increased the step size up to 0.1 ps, i still get the same result. Thanks, Nihal On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz <enihalkork...@gmail.com>wrote: > Dear all, > > I am trying to simulate a GB simulation of a 112 amino acid long protein. I > keep getting these errors, > > Step 27718, time 55.436 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 33.319842, max 438.763717 (between atoms 79 and 81) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > Step 27718, time 55.436 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.058237, max 1.390675 (between atoms 91 and 93) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 91 92 50.2 0.1016 0.1065 0.1010 > 91 93 90.0 0.1002 0.2415 0.1010 > 91 94 70.2 0.1025 0.1066 0.1010 > 79 80 90.0 0.1057 1.0667 0.1090 > 79 81 90.0 1.3066 47.9342 0.1090 > 85 86 90.0 0.1084 0.1758 0.1090 > 85 87 90.0 1.0654 0.1668 0.1090 > 88 89 90.0 0.1097 0.6994 0.1090 > 88 90 90.0 0.1125 0.1097 0.1090 > 91 92 50.2 0.1016 0.1065 0.1010 > 91 93 90.0 0.1002 0.2415 0.1010 > 91 94 70.2 0.1025 0.1066 0.1010 > > > I am copying my mdp parameters below, I'd appreciate any suggestions to fix > that. > > integrator = sd > tinit = 0 > dt = 0.002 > nsteps = 2500000 > simulation_part = 1 > init_step = 1 > > nstxout = 5000 > nstvout = 5000 > nstenergy = 500 > nstxtcout = 500 > nstlog = 500 > > xtc_grps = System > energygrps = System > comm_mode = Linear > ; neighbor searching and vdw/pme setting up > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 2.0 > > implicit_solvent = GBSA > gb_algorithm = OBC > gb_saltconc = 0.15 > rgbradii = 2.0 > > coulombtype = Cut-off > fourierspacing = 0.1 > pme_order = 6 > rcoulomb = 2.0 > > vdwtype = Cut-off > rvdw_switch = 1.0 > rvdw = 2.0 > > ; cpt control > tcoupl = V-rescale > tc-grps = System > tau_t = 0.1 > ref_t = 300.0 > > Pcoupl = Berendsen > pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > ; velocity & temperature control > gen_vel = yes > gen_temp = 300.0 > annealing = no > constraints = hbonds > constraint_algorithm = lincs > morse = no > > > Thanks, > -- > Elif Nihal Korkmaz > > Research Assistant > University of Wisconsin - Biophysics > Member of Qiang Cui & Thomas Record Labs > 1101 University Ave, Rm. 8359 > Madison, WI 53706 > Phone: 608-265-3644 > Email: kork...@wisc.edu > > > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu
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