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....@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+s5086n5010324...@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 >> 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. >> -- >> gmx-users mailing list [hidden >> email]<http://user/SendEmail.jtp?type=node&node=5010324&i=0> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [hidden >> email]<http://user/SendEmail.jtp?type=node&node=5010324&i=1>. >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://gromacs.5086.x6.nabble.com/restraint-lambdas-for-position-restraints-in-hamiltonian-exchange-tp5010322p5010324.html >> To unsubscribe from restraint-lambdas for position restraints in >> hamiltonian exchange, click >> here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5010322&code=ZGVqdW4ubGluQGdtYWlsLmNvbXw1MDEwMzIyfDE0MzAxNDIxNA==> >> . >> NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> >> > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/restraint-lambdas-for-position-restraints-in-hamiltonian-exchange-tp5010322p5010325.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists