[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 02:12:57 CEST 2010

C Johnson wrote:
> 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 don't see the need for -shuffle, but yes, that's more or less the right way to 
create an 8-peptide grid.

> 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 :)

Well, what's in your em.mdp file?  It could be that there is horrendous atomic 
overlap that even EM can't resolve.  But you can easily determine that by 
looking at the coordinate file that you used as input into grompp.  I don't see 
the relationship to the system you build (did_it_work.pdb) and the coordinate 
file passed to grompp (b4em), so it could be that something you did in between 
messed up the system, but in that case you haven't told us everything you've 
done and it makes it hard (impossible) to give you solid advice.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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