[gmx-users] force field parameters/B state dihedrals
dmobley at gmail.com
Fri Jul 21 00:07:35 CEST 2006
I'm setting up some relative free energy calculations involving
changing atom types, and I have a related question about topologies.
In the dihedrals section, if my force field contains parameters for
the dihedral states organized by bond type, these are automatically
filled in when no parameters are specified in the topology.
On the other hand, if I specify parameters in the topology file for A
and B states, these are use instead of those specified for the force
What happens if I specify parameters in the topology file for only the
A state? Does the B state:
(a) automatically use the parameters specified by the A state, or
(b) first check the force field for parameters, only using those
specified by the A state if it finds none?
I know that in cases where I specify parameters for only the A state,
and none are found in the force field, the B state uses the same A
state parameters. My question is what happens when B state parameters
could be specified by the force field, as this seems somewhat
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