- what is the difference between equivalence auto and equivalence in the field file?
- does enhanced monte carlo find all dihedral combinations?
- if I change a name in equivalence auto the forcefield rule gets applied according to the way i want however if i change it in the equivalence part it doesnt happen
- how do I know which rule is applied to which atom?
- even if some angle parameters are missing sometimes emc runs how is that possible?
- what are the recommendations to ease forcefield typing?
To answer your questions in the same listed manner:
- The ‘auto’ label refers to general parameters. In some force fields, you will find general parameters for bonds, angles, dihedral, and improper contributions. These are reflected by e.g.
ITEM BOND_AUTOas opposed to
ITEM BOND. The
ITEM EQUIVALENCEsection applies to
ITEM BONDetc. only, as the
ITEM EQUIVALENCE_AUTOsection applies to
ITEM BOND_AUTOetc. sections only. In general, all paragraphs ending in
_AUTObelong together. Typically, types defining the table entry can have wild cards in the form of an
- EMC uses site connectivity to determine all bond, angle, dihedral, and improper contributions by means of a recursive algorithm, which walks the connectivity tree.
- This point cannot be answered definitively without explicit examples.
- EMC types by groups. You can switch on force field debugging by setting the option
full, depending on how much output you would like EMC to generate. The output states the group and the group site to which EMC is applying rules. Subsequently, – when selecting
full– EMC also outputs how it is applying rules.
- Most likely you are referring to a case, in which EMC selects general parameters from the ‘auto’ lists. EMC first searches for occurrence in the list of specific parameters (i.e. the parameter sections without
_AUTO). When no specific parameter is found, EMC will search the general list of parameters, with full use of wild cards.
- I am not quite sure, what you mean by ‘ease force field typing’. Could you elaborate?
In general, EMC internally sorts the list of rules within each type starting with the most complex rule first. EMC selects the first rule matching the regarded chemical environment. The precedence of a rule (i.e. the order in which rules are to be applied) is controlled by the
ITEM PRECEDENCES section.