Re: [gmx-users] Replica Exchange with Solute Tempering

2013-10-28 Thread Andrew Ritchie
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 coulom

Re: [gmx-users] Replica Exchange with Solute Tempering

2013-10-26 Thread HANNIBAL LECTER
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 lambda

Re: [gmx-users] Replica Exchange with Solute Tempering

2013-10-26 Thread David Osguthorpe
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 pl

Re: [gmx-users] Replica Exchange with Solute Tempering

2013-10-26 Thread Michael Shirts
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

[gmx-users] Replica Exchange with Solute Tempering

2013-10-26 Thread David Osguthorpe
Hi Ive been looking for a sample input for a REST simulation but so far have not been able to find one. Does anybody have an example to share? Ive seen the tutorial by Mark which mentions REST but I dont see this included in the archived examples. Am I missing something? Thanks for any help