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