[gmx-users] large charge group

Sunjoo Lee sunnytov at gmail.com
Wed Nov 19 17:01:01 CET 2008

Hello All

Recently I have figured out the biggest problem that made my system unstable.
I have parameterized a molecule pretty similar to octane. A single
charge group used to be assigned to this molecule. With 1 nm cut-off
distance for LJ interaction and the direct space for electrostatic
interaction, the system underwent severe volume fluctuation and at the
end crashed due to enormously large short range coulomb interaction
energy. The problem was temporarily resolved by using greater cut-off
distance such as 1.4 nm. But this fixation was not perfect when I put
this molecule into more complex system. Regardless of the cut-off
distance even to 1.8 nm did not solve the problem. The simulation
always terminated due to large coulomb energy even though no direct
contact or any weird structure was observed at that snapshot.

With the help of many experts, I have made a single charge group into
three smaller charge group, which magically fixed all the problem that
I have had for almost 2 years. I know that charge group is only used
for neighbor search. Can anybody tell me how the size of charge group
can influence the interaction between atoms depending on the
complexity of the system and cut-off distance??

Thank you in advance


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