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
