[gmx-users] Re: free energy calculation , grompp crash
lidawei at gmail.com
Tue Feb 8 17:24:57 CET 2011
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
state of the molecule corresponds to the proper vacuum state without
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?
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