[gmx-users] restraint-lambdas for position restraints in hamiltonian exchange
mrshirts at gmail.com
Sat Aug 3 22:26:31 CEST 2013
Short answer is anything that has a B state parameter can be included
in in Hamiltonian exchange.
If it's pull code or explicit restraints, it's controlled by restraint lambda.
> I went through the manual and couldn't find any definite answers to the
> following questions.
> First, I wonder if the reference positions of position restraints, not just
> the force constants, of different replicas are exchanged in hamiltonian
> exchange based on restraint-lambdas? For example, if I have 1 molecule that
> has 2 structures, say, A and B and the following 2-component
> restraint-lambdas: 1.0 1.0 with replica 0 starting in A and replica 1 in B,
> would the exchange between replica 0 and 1 yield anything meaningful ?
Right now, the pull code doesn't have B state positions, just force
constants. It CAN be done using distance restraints, but then you have
to make the atoms involved part of the same molecule. Adding B state
distances to pull code was recently requested, and will probably be
straightforward to put in soon.
> other word, would the relaxation towards the other structure occur in both
> states once an exchange was accepted?
> Another question is what types of restraints can restraint-lambdas act on?
> For example, bond/angle/distance/position restraints, COM-pulling potential
Anything with a B state in gromacs topologies.
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