[gmx-users] Re: free energy calculation , grompp crash

[Da-Wei Li]

hello

Now it is almost clear what happened. When couple-intramol is no (default),
all pairwise vdm and charge interaction becomes bonded interaction.


 All intra-molecular non-bonded interactions for moleculetype couple-moltype

are replaced by exclusions and explicit pair interactions. In this manner
the decoupled

state of the molecule corresponds to the proper vacuum state without
periodicity

effects.


But there is still one thing I don't fully understand. Mdrun will complain
"Warning: 1-4 interaction between 1 and 114 at distance 2.035 which is
larger than the 1-4 table size 2.000 nm". I guess is that every pair wiii
have 1-4 interaction because every pair (except exclusion) becomes bonded
interaction. These fake 1-4 are not calculated as an 1-4 interaction so that
I can neglect this warning, right?


thanks.


dawei
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