Greetings, I would also be interested in an example of using REST via Hamiltonian REMD in the current gromacs build. I'm particularly interested in enhanced conformational sampling of 160-270 residue proteins. As it stands, I've been unable to achieve any appreciable exchange probability in coulomb or vdw lambdas without resorting to changing the lambda values by +/- 0.02 or less and am hoping ST will allow me to increase the spacing between lambdas. Thanks for any help, Andrew
On Sat, Oct 26, 2013 at 9:45 PM, HANNIBAL LECTER <hanniballecte...@gmail.com > wrote: > Hi > I had tried using gromacs-4.6.1 to perform solute tempering. If you go > through terakawa's paper you have to describe the lambdas corresponding to > the temperatures. In your topology file define the params corresponding to > the two end states l=0 and l=1. Then define vdw, bonded and coulomb lambdas > in the mdp file. The format is very well described in the manual. Then just > the regular -replex syntax would perform solute tempering. However, the > free energy module required to perform this, is extremely slow. > On Oct 26, 2013 8:46 PM, "David Osguthorpe" <david.osgutho...@gmail.com> > wrote: > > > On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote: > > > Hi, all- > > > > > > Rest essentially scales the solute-solvent interactions, but maintains > > > the solute-solute interactions. This can be done solely with > > > Hamiltonian replica exchange, which is in 4.6. It's a bit tricky, > > > though. We plan on having something that does this automatically in > > > 5.0 or 5.1, but it's not there yet. > > > > > > What do you intend to do? It could be that there's a better way to do > > > what you want to do with Hamiltonian replica exchange, as well. > > > > > > > Sorry - yes Im looking for an example of how to do REST via Hamiltonian > > replica exchange > > > > Ive seen the papers by Moors (Improved Replica Exchange Method for > > Native-State Protein Sampling) > > and Terekawa (On easy implementation of a variant of the replica exchange > > with solute tempering in GROMACS) > > and followed some of the gromacs user list discussions from 2011 on REST > > simulations > > > > As you say, it looks like its "a bit tricky" so was hoping there was a > toy > > example > > somewhere > > > > Thanks > > > > David > > -- > > 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 > -- -Andrew Ritchie -- 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