[gmx-users] Question about redundancy in forcefield files and dihedral parameterization
ericsmoll at gmail.com
Tue Jul 28 20:41:30 CEST 2015
Hello GROMACS users,
In the *types directives, what impact does redundancy have? Does a later
specification override an earlier specification? For a concrete example,
consider a bondtypes entry:
[ bondtypes ]
A B 1 1.0 2.0
A B 1 1.0 3.0
Which specification will be used?
What impact does arrangement redundancy have on dihedral parameters? Will
the equivalent specifications shown below cause problems?
[ dihedraltypes ]
A B B C 3 1.0 2.0 3.0 4.0 5.0 6.0
C B B A 3 1.0 2.0 3.0 4.0 5.0 6.0
C B B A 3 1.0 2.0 3.0 4.0 5.0 600.0
When computing dihedral parameters of small symmetric molecules using ab
initio calculations, does one divide the weight or amplitude of the
LJ-subtracted dihedral potential across equivalent dihedrals along the same
bond? For example, does the computed dihedral spectrum of ethane (H-C-C-H)
get divided by 9?
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