[gmx-users] Re Multiple Chains

C Johnson helstreak at hotmail.com
Thu Sep 16 02:06:01 CEST 2010

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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