[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange
dejun.lin at gmail.com
Sun Aug 4 00:12:08 CEST 2013
So I take it that in the position restraint case (not COM-pulling), where
the reference positions are determined by the starting structure instead of
a B-state topology, the reference positions won't be swapped ?
2013/8/3 Michael Shirts-2 [via GROMACS] <
ml-node+s5086n5010324h43 at n6.nabble.com>
> 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
> > 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
> > the force constants, of different replicas are exchanged in hamiltonian
> > exchange based on restraint-lambdas? For example, if I have 1 molecule
> > 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.
> > In
> > other word, would the relaxation towards the other structure occur in
> > states once an exchange was accepted?
> > Another question is what types of restraints can restraint-lambdas act
> > For example, bond/angle/distance/position restraints, COM-pulling
> > ?
> Anything with a B state in gromacs topologies.
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