Samik Bhattacharya wrote:
hi,
Justin, i have completed upto the genion step of that simulation. One
error is creeping in this step which is nonzero system charge. my system
is said to have a charge 1.69. now how to neutralize this kind of broken
charge? another thing is that how this kind of broken chage is being
developed? i think something was wrong in previous steps. but can't
recognise which step to account for this anomalous behavior? waiting for
your valuable suggestions...
Probably you have broken termini. Go and read all of the output from
pdb2gmx carefully. If that doesn't clue you in, look at the [atoms]
section of your .top file. There's a running count of the total
charge... whenever that first becomes non-integral for the last atom in
a residue, you have a broken residue there.
Mark
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