Dear all I am doing simulation of dna -protein complex . in this processing I am getting error in energy minimisation step-
the error comes like this- There were 2 inconsistent shifts. Check your topology There were 4 inconsistent shifts. Check your topology Steepest Descents: Tolerance (Fmax) = 1.00000e+02 Number of steps = 10000 There were 6 inconsistent shifts. Check your topology Warning: 1-4 interaction between 1 and 6 at distance 7.731 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size There were 6 inconsistent shifts. Check your topology= inf, atom= 479 ------------------------------------------------------- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 10648 ] -------------------------------------------------- My em.mdp file is like this- cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001 nsteps = 10000 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ can anyone suggest how can i get rid from this problem. Thanks a lot in advance. Nitu sharma
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