[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange

[Dejun Lin]

Hi Micheal,

Sorry for keep bugging you about this but I want to make sure I'm doing
what I think I'm doing :)
I did some test on the following setup.

restraint-lambdas = 0.3 0.299999 (essentially no difference) on position
restraints.
replica 0 starts in structure A and replica 1 in structure B. The 2
position restraints have exactly the same set of force constants, i.e., the
2 replica used the same top/itp file.
But each of this 2 replicas should have one distinct set of restraints
because the difference in initial structure (gro file) are huge.

Replica 0:  structure *A*, restraints A (ref. position A, force constant C)
Replica 1:  structure *B*, restraints B (ref. position B, force constant C)

Swapped between the 2 replica were observed and I looked at the trajectory
from *replica 0* in VMD and noticed that there were *structure B* in it.

Can assume that swap resulted in the following states ?

Replica 0:  structure *B*, restraints A (ref. position A, force constant C)
Replica 1:  structure *A*, restraints B (ref. position B, force constant C)

i.e. It was the coordinates instead of lambda values were swapped between
replicas, which is essentially the same as if the reference positions were
swapped.

Thanks again for your help!

-Dejun


2013/8/3 Michael Shirts-2 [via GROMACS] <
ml-node+s5086n5010326h5 at n6.nabble.com>

> That is correct. Such a functionality wouldn't be that hard to
> implement - but there are a long list of easy functionalities to be
> implemented. You can submit a request to redmine.gromacs.org so that
> the request is archived.
>
> On Sat, Aug 3, 2013 at 6:12 PM, Dejun Lin <[hidden email]<http://user/SendEmail.jtp?type=node&node=5010326&i=0>>
> wrote:
>
> > 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] <
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=5010326&i=1>>
> >
> >> 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.
> >>
> >> > In
> >> > 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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