[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange
mrshirts at gmail.com
Sun Aug 4 00:36:53 CEST 2013
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 <dejun.lin at gmail.com> 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] <
> 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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