Sorry guys, I'm still learning the lingo.
I want to simulate multiple molecules.
This is what I tried:
genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb
Does this even seem like the right thing to do?
I got to this part:
grompp -v -f em -c b4em -o em -p speptide
mdrun -v -s em -o em -c after_em -g emlog
But I get an error that essentially tells me that my system needs to be energy
minimized:
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 .. 150 ]
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 :)
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