[gmx-users] pdb2gmx and periodic molecule

[Alex]

JL> The force field parameters for a phosphodiester are the same in a linear, finite
JL> DNA as they will be in your infinite chain.

I didn't mean that anything would need to be changed in the description of residues. The FF handles a
finite chain perfectly.

JL> The problem is in telling pdb2gmx
JL> "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)."

This is exactly what I meant, the linking. Is there a way to achieve this
without messing with the code? I just haven't looked at the code, so
if you think I'm being a cheeky little bastard, I'll accept that. :)

Thanks,

Alex