[gmx-users] Re Multiple Chains

C Johnson helstreak at hotmail.com
Thu Sep 16 02:36:06 CEST 2010

Sorry, I sent the wrong steps.  This is what I did in order to get the range checking error:

genconf -f polygly.pdb -nbox 2 2 2 -shuffle  -o did_it_work.pdb

pdb2gmx -f did_it_work.pdb -p did_it_work.top -o did_it_work

0: GROMOS96 43a1 force field

editconf -f did_it_work -o -d 1.0

genbox -cp out -cs -p did_it_work -o b4em

grompp -v -f em -c b4em -o em -p did_it_work

The em.mdp is from the speptide tutorial.

mdrun -v -s em -o em -c after_em -g emlog

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 ]

Thanks guys for your help and sorry if I'm frustrating you.
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