<div id="RTEContent"> Hello,<br> <br> I am trying to run a simulation on an infinite silicon surface. We built the structure from a unit cell and used X2top with pbc option to generate a framework for the itp file. Bonds, angles and dihedrals were generated in prodrg and the ffG43a1bon.itp file was edited to include these additions. Currently, we are trying to run an energy minimzation on the system and are running into the following error:<br> <br> Back Off! I just backed up mem1out.log to ./#mem1out.log.3#<br> Getting Loaded...<br> Reading file gem1out.tpr, VERSION 3.3 (single precision)<br> Loaded with Money<br> <br> <br> Back Off! I just backed up mem1out.edr to ./#mem1out.edr.3#<br> Polak-Ribiere Conjugate Gradients:<br> Tolerance (Fmax) = 1.00000e+03<br>
Number of steps = 5000<br> F-max = 1.13638e+08 on atom 59586<br> F-Norm = nan<br> <br> -------------------------------------------------------<br> Program mdrun, VERSION 3.3<br> Source code file: nsgrid.c, line: 226<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 .. 11875 ]<br> Please report this to the mailing list (gmx-users@gromacs.org)<br> -------------------------------------------------------<br> <br> "I'm Your Worst Nightmare" (Creep)<br> <br> Halting program mdrun<br> <br> gcq#38: "I'm Your Worst Nightmare" (Creep)<br> <br> We have looked at the data to make sure that we havent created any overlapping atomic coordinates and also made sure the system charge is 0.<br> <br> Any suggestions as to the cause of the error?<br> <br> Morgan<br>
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