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Sorry guys, I'm still learning the lingo.<br><br>I want to simulate multiple molecules.<br><br>This is what I tried:<br><br>genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb<br><br>Does this even seem like the right thing to do?<br><br>I got to this part:<br><font style="" color="#000000"><br></font><font style="font-size: 10pt;" size="2" color="#000000" face="Tahoma">grompp -v -f em -c b4em -o em -p speptide
</font><font style="font-size: 10pt;" size="2" color="#000000" face="Tahoma"><br></font><font style="font-size: 10pt;" size="2" color="#000000" face="Tahoma">mdrun -v -s em -o em -c after_em -g emlog
</font><br><br>But I get an error that essentially tells me that my system needs to be energy minimized:<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 .. 150 ]<br><br><br>I'm guessing I'm pretty wrong in my approach to adding multiple molecules based on a single molecule pdb file. I'm determined to get this :)<br><br><br> </body>
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